#/*########################################################################## # # The PyMca X-Ray Fluorescence Toolkit # # Copyright (c) 2004-2020 European Synchrotron Radiation Facility # # This file is part of the PyMca X-ray Fluorescence Toolkit developed at # the ESRF by the Software group. # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # #############################################################################*/ __author__ = "V.A. Sole - ESRF Data Analysis" __contact__ = "sole@esrf.fr" __license__ = "MIT" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" import sys import os import numpy import types import logging import time from PyMca5.PyMcaCore import DataObject from PyMca5.PyMcaIO import specfilewrapper as specfile _logger = logging.getLogger(__name__) SOURCE_TYPE = "SpecFile" # Scan types # ---------- SF_EMPTY = 0 # empty scan SF_SCAN = 1 # non-empty scan SF_MESH = 2 # mesh scan SF_MCA = 4 # single mca SF_NMCA = 8 # multi mca (more than 1 mca per acq) SF_UMCA = 16 # mca number does not match pts number class SpecFileDataSource(object): Error= "SpecFileDataError" def __init__(self, nameInput): if type(nameInput) == type([]): nameList = nameInput else: nameList = [nameInput] if len(nameList) > 1: #who knows if one day will make selections thru several files... raise TypeError("Constructor needs string as first argument") if sys.version < '3.0': testTypes = [types.StringType, types.UnicodeType] else: testTypes = [type("")] for name in nameList: if type(name) not in testTypes: raise TypeError("Constructor needs string as first argument") self.sourceName = nameInput self.sourceType = SOURCE_TYPE self.__sourceNameList = nameList self.__source_info_cached = None self.refresh() def refresh(self): self._sourceObjectList = [] self.__fileHeaderList = [] #for name in self.__sourceNameList: # if not os.path.exists(name): # raise ValueError("File %s does not exists" % name) for name in self.__sourceNameList: self._sourceObjectList.append(specfile.Specfile(name)) self.__fileHeaderList.append(False) self.__lastKeyInfo = {} def getSourceInfo(self): """ Returns information about the specfile object created by the constructor to give application possibility to know about it before loading. Returns a dictionary with the key "KeyList" (list of all available keys in this source). Each element in "KeyList" has the form 'n1.n2' where n1 is the scan number and n2 the order number in file starting at 1. """ return self.__getSourceInfo() def __getSourceInfo(self): scanlist=self.__getScanList() source_info={} source_info["Size"] = len(scanlist) source_info["KeyList"] = scanlist source_info["SourceType"] = SOURCE_TYPE HAS_CACHED_INFO = False if self.__source_info_cached: if self.__source_info_cached["SourceName"] == self.__sourceNameList[0]: HAS_CACHED_INFO = True num_mca = [] num_pts = [] commands = [] sf_type = [] for i in scanlist: CACHE_INDEX = None if HAS_CACHED_INFO: if i in self.__source_info_cached["KeyList"]: if i != self.__source_info_cached["KeyList"][-1]: # information in cache and it was not the last scan # at that time. We can use the cached information self.__fileHeaderList[0] = self.__source_info_cached["FileHeader"] CACHE_INDEX = self.__source_info_cached["KeyList"].index(i) if CACHE_INDEX is not None: # it can be 0 and still use the cache num_mca.append(self.__source_info_cached["NumMca"][CACHE_INDEX]) num_pts.append(self.__source_info_cached["NumPts"][CACHE_INDEX]) commands.append(self.__source_info_cached["Commands"][CACHE_INDEX]) continue sel=self._sourceObjectList[0].select(i) if self.__fileHeaderList[0] == False: try: self.__fileHeaderList[0] = sel.fileheader('') except: _logger.debug("getSourceInfo %s", sys.exc_info()[1]) self.__fileHeaderList[0] = None try: n = sel.nbmca() except: n = 0 num_mca.append(n) try: n = sel.lines() except: n= 0 num_pts.append(n) try: n = sel.command() except: n= "" commands.append(n) source_info["SourceName"] = self.__sourceNameList[0] source_info["FileHeader"] = self.__fileHeaderList[0] source_info["NumMca"] = num_mca source_info["NumPts"] = num_pts source_info["Commands"] = commands source_info["ScanType"] = list(map(self.__getScanType, num_pts, num_mca, commands)) self.__source_info_cached = source_info return source_info def __getScanList(self): aux= self._sourceObjectList[0].list().split(",") newlistcount=[] newlist=[] for i in aux: if not (":" in i): start_index=end_index=int(i) else: s= i.split(":") start_index=int(s[0]) end_index=int(s[1]) for j in range(start_index,end_index+1): newlist.append(j) newlistcount.append(newlist.count(j)) for i in range(len(newlist)): newlist[i]="%d.%d" % (newlist[i],newlistcount[i]) return newlist def __getScanType(self, num_pts, num_mca, command): stype= SF_EMPTY if num_pts>0: if command is None: stype= SF_SCAN elif "mesh" in command: stype= SF_MESH else: stype= SF_SCAN if num_mca%num_pts: stype+= SF_UMCA elif num_mca==num_pts: stype+= SF_MCA elif num_mca>0: stype+= SF_NMCA else: if num_mca==1: stype= SF_MCA elif num_mca>1: stype= SF_NMCA return stype def getKeyInfo (self, key): """ If key given returns information of a perticular key. """ fileName = self.__sourceNameList[0] key_type= self.__getKeyType(key) if key_type=="scan": scan_key= key elif key_type=="mca": (scan_key, mca_no)=self.__getMcaPars(key) key_info = self.__getScanInfo(scan_key) if os.path.exists(fileName): self.__lastKeyInfo[key] = os.path.getmtime(fileName) else: self.__lastKeyInfo[key] = key_info["Lines"] + \ key_info["NbMca"] return key_info def __getKeyType (self,key): count= key.count('.') if (count==1): return "scan" elif (count==2) or (count==3): return "mca" else: raise KeyError("SpecFileDataSource: Invalid key") def __getScanInfo(self, scankey): index = 0 sourceObject = self._sourceObjectList[index] scandata= sourceObject.select(scankey) info={} info["SourceType"] = SOURCE_TYPE #doubts about if refer to the list or to the individual file info["SourceName"] = self.sourceName info["Key"] = scankey info['FileName'] = self.__sourceNameList[index] if self.__fileHeaderList[index] == False: try: self.__fileHeaderList[index] = scandata.fileheader('') except: _logger.debug("getScanInfo %s", sys.exc_info()[1]) self.__fileHeaderList[index] = None info["FileHeader"] = self.__fileHeaderList[index] try: info["Number"] = scandata.number() except: info["Number"] = None try: info["Order"] = scandata.order() except: info["Order"] = None try: info["Cols"] = scandata.cols() except: info["Cols"] = 0 try: info["Lines"] = scandata.lines() except: info["Lines"] = 0 try: info["Date"] = scandata.date() except: info["Date"] = None if hasattr(scandata, "allmotors"): try: info["MotorNames"] = scandata.allmotors() except: info["MotorNames"] = None else: try: info["MotorNames"] = sourceObject.allmotors() except: info["MotorNames"] = None try: info["MotorValues"] = scandata.allmotorpos() except: info["MotorValues"] = None try: info["LabelNames"] = scandata.alllabels() except: info["LabelNames"] = [] try: info["Command"] = scandata.command() except: info["Command"] = None try: info["Header"] = scandata.header("") except: info["Header"] = None try: info["NbMca"] = scandata.nbmca() except: info["NbMca"] = 0 try: info["hkl"] = scandata.hkl() except: info["hkl"] = None if info["NbMca"]: if info["Lines"] > 0 and info["NbMca"] % info["Lines"] == 0: info["NbMcaDet"]= info["NbMca"] // info["Lines"] else: info["NbMcaDet"]= info["NbMca"] info["ScanType"]= self.__getScanType(info["Lines"], info["NbMca"], info["Command"]) return info def __getMcaInfo(self, mcano, scandata, info=None): if info is None: info = {} mcainfo= {} if "NbMcaDet" in info: det= info["NbMcaDet"] if info["Lines"]>0: mcainfo["McaPoint"]= int(mcano/info["NbMcaDet"])+(mcano%info["NbMcaDet"]>0) mcainfo["McaDet"]= mcano-((mcainfo["McaPoint"]-1)*info["NbMcaDet"]) try: mcainfo["LabelValues"]= scandata.dataline(mcainfo["McaPoint"]) except: mcainfo["LabelValues"]= None else: mcainfo["McaPoint"]= 0 mcainfo["McaDet"]= mcano mcainfo["LabelValues"]= None calib= scandata.header("@CALIB") mcainfo["McaCalib"]=[0.0,1.0,0.0] if len(calib): if len(calib) == info["NbMcaDet"]: calib = [calib[mcainfo["McaDet"]-1]] else: _logger.debug("Number of calibrations does not match number of MCAs") if len(calib) == 1: pass else: raise ValueError("Number of calibrations does not match number of MCAs") ctxt= calib[0].split() if len(ctxt)==4: #try: if 1: cval= [ float(ctxt[1]), float(ctxt[2]), float(ctxt[3]) ] mcainfo["McaCalib"]= cval else: #except: mcainfo["McaCalib"]=[0.0,1.0,0.0] ctime= scandata.header("@CTIME") if len(ctime): if len(ctime) == info["NbMcaDet"]: ctime = [ctime[mcainfo["McaDet"]-1]] else: _logger.debug("Number of counting times does not match number of MCAs") if len(ctime) == 1: pass else: raise ValueError("Number of counting times does not match number of MCAs") ctxt= ctime[0].split() if len(ctxt)==4: try: mcainfo["McaPresetTime"]= float(ctxt[1]) mcainfo["McaLiveTime"]= float(ctxt[2]) mcainfo["McaRealTime"]= float(ctxt[3]) except: pass chann = scandata.header("@CHANN") if len(chann): if len(chann) == info["NbMcaDet"]: chann = [chann[mcainfo["McaDet"] - 1]] else: _logger.debug("Number of @CHANN information does not match number of MCAs") if len(chann) == 1: pass else: raise ValueError("Number of @CHANN information does not match number of MCAs") ctxt= chann[0].split() if len(ctxt)==5: mcainfo['Channel0'] = float(ctxt[2]) else: mcainfo['Channel0'] = 0.0 else: mcainfo['Channel0'] = 0.0 return mcainfo def __getMcaPars(self,key): index = 0 nums= key.split('.') size = len(nums) sel_key = nums[0] + "." + nums[1] if size==3: mca_no=int(nums[2]) elif size==4: sel=self._sourceObjectList[index].select(sel_key) try: lines = sel.lines() except: lines=0 if nums[3]==0: mca_no=int(nums[2]) else: mca_no=((int(nums[3])-1)*lines)+int(nums[2]) else: raise KeyError("SpecFileData: Invalid key") return (sel_key,mca_no) def getDataObject(self,key,selection=None): """ Parameters: * key: key to be read from source. It is a string using the following formats: "s.o": loads all counter values (s=scan number, o=order) - if ScanType==SCAN: in a 2D array (mot*cnts) - if ScanType==MESH: in a 3D array (mot1*mot2*cnts) - if ScanType==MCA: single MCA in 1D array (0:channels) "s.o.n": loads a single MCA in a 1D array (0:channels) - if ScanType==NMCA: n is the MCA number from 1 to N - if ScanType==SCAN+MCA: n is the scan point number (from 1) - if ScanType==MESH+MCA: n is the scan point number (from 1) "s.o.p.n": loads a single MCA in a 1D array (0:channels) - if ScanType==SCAN+NMCA: p is the point number in the scan n is the MCA device number - if ScanType==MESH+MCA: p is first motor index n is second motor index "s.o.MCA": loads all MCA in an array - if ScanType==SCAN+MCA: 2D array (pts*mca) - if ScanType==NMCA: 2D array (mca_det*mca) - if ScanType==MESH+MCA: 3D array (pts_mot1*pts_mot2*mca) - if ScanType==SCAN+NMCA: 3D array (pts_mot1*mca_det*mca) - if ScanType==MESH+NMCA: creates N data page, one for each MCA device, with a 3D array (pts_mot1*pts_mot2*mca) """ key_type= self.__getKeyType(key) if key_type=="scan": scan_key= key elif key_type=="mca": (scan_key, mca_no)=self.__getMcaPars(key) if self.__source_info_cached is None: sourceinfo = self.getSourceInfo() sourcekeys = sourceinfo['KeyList'] else: sourceinfo = self.__source_info_cached sourcekeys = sourceinfo['KeyList'] if scan_key not in sourcekeys: sourceinfo = self.getSourceInfo() sourcekeys = sourceinfo['KeyList'] if scan_key not in sourcekeys: raise KeyError("Key %s not in source keys" % key) mca3D = False _logger.debug("SELECTION = %s", selection) _logger.debug("key_type = %s", key_type) if key_type == "scan": if selection is not None: if 'mcalist' in selection: mca3D = True if (key_type=="scan") and (not mca3D): output = self._getScanData(key, raw = True) output.x = None output.y = None output.m = None output.info['selection'] = selection if selection is None: output.info['selectiontype'] = "2D" return output elif type(selection) != type({}): #I only understand index selections raise TypeError("Only selections of type {x:[],y:[],m:[]} understood") else: if 'x' in selection: indexlist = [] for labelindex in selection['x']: if labelindex != 0: if 'cntlist' in selection: label = selection['cntlist'][labelindex] else: label = output.info['LabelNames'][labelindex] else: label = output.info['LabelNames'][labelindex] if label not in output.info['LabelNames']: raise ValueError("Label %s not in scan labels" % label) index = output.info['LabelNames'].index(label) if output.x is None: output.x = [] output.x.append(output.data[:, index]) indexlist.append(index) output.info['selection']['x'] = indexlist if 'y' in selection: indexlist = [] for labelindex in selection['y']: if 'cntlist' in selection: label = selection['cntlist'][labelindex] else: label = output.info['LabelNames'][labelindex] if label not in output.info['LabelNames']: raise ValueError("Label %s not in scan labels" % label) index = output.info['LabelNames'].index(label) if output.y is None: output.y = [] output.y.append(output.data[:, index]) indexlist.append(index) output.info['selection']['y'] = indexlist if 'm' in selection: indexlist = [] for labelindex in selection['m']: if 'cntlist' in selection: label = selection['cntlist'][labelindex] else: label = output.info['LabelNames'][labelindex] if label not in output.info['LabelNames']: raise ValueError("Label %s not in scan labels" % label) index = output.info['LabelNames'].index(label) if output.m is None: output.m = [] output.m.append(output.data[:, index]) indexlist.append(index) output.info['selection']['m'] = indexlist output.info['selection']['cntlist'] = output.info['LabelNames'] output.info['selectiontype'] = "1D" if output.x is not None: output.info['selectiontype'] = "%dD" % len(output.x) output.data = None elif key_type=="mca": output = self._getMcaData(key) selectiontype = "1D" if selection is not None: selectiontype = selection.get('selectiontype', "1D") output.info['selectiontype'] = selectiontype if output.info['selectiontype'] not in ['2D', '3D', 'STACK']: ch0 = int(output.info['Channel0']) output.x = [numpy.arange(ch0, ch0 + len(output.data)).astype(numpy.float64)] output.y = [output.data[:].astype(numpy.float64)] output.m = None output.data = None else: output.x = None output.y = None output.m = None output.data = None npoints = output.info['NbMca'] // output.info['NbMcaDet'] index = 0 scan_obj = self._sourceObjectList[index].select(scan_key) SPECFILE = True if isinstance(self._sourceObjectList[index], specfile.specfilewrapper): SPECFILE = False for i in range(npoints): if SPECFILE: wmca_no= mca_no + output.info['NbMcaDet'] * i mcaData= scan_obj.mca(wmca_no) else: mca_key = '%s.%d' % (scan_key, mca_no) mcaData = self._getMcaData(mca_key).data if i == 0: nChannels = mcaData.shape[0] output.data = numpy.zeros((npoints, nChannels), numpy.float32) output.data[i,:] = mcaData #I have all the MCA data ready for image plot if selectiontype == 'STACK': output.data.shape = 1, npoints, -1 shape = output.data.shape for i in range(len(shape)): key = 'Dim_%d' % (i+1,) output.info[key] = shape[i] output.info["SourceType"] = "SpecFileStack" output.info["SourceName"] = self.sourceName output.info["Size"] = shape[0] * shape[1] output.info["NumberOfFiles"] = 1 output.info["FileIndex"] = 1 elif (key_type=="scan") and mca3D: output = self._getScanData(key, raw = True) output.x = None output.y = None output.m = None #get the number of counters in the scan if 'cntlist' in selection: ncounters = len(selection['cntlist']) else: ncounters = output.info['LabelNames'] # For the time being assume only one mca can be selected detectorNumber = selection['y'][0] - ncounters #read the first mca data of the first point mca_key = '%s.%d.%d' % (key, 1+detectorNumber, 1) mcaData = self._getMcaData(mca_key) ch0 = int(mcaData.info['Channel0']) calib = mcaData.info['McaCalib'] nChannels = float(mcaData.data.shape[0]) channels = numpy.arange(nChannels) + ch0 #apply the calibration channels = calib[0] + calib[1] * channels +\ calib[2] * channels * channels ones =numpy.ones(nChannels) #get the different x components xselection = selection.get('x', []) if len(xselection) != 2: raise ValueError("You have to select two X axes") indexlist = [] for labelindex in xselection: if labelindex != 0: if 'cntlist' in selection: label = selection['cntlist'][labelindex] else: label = output.info['LabelNames'][labelindex] else: label = output.info['LabelNames'][labelindex] if label not in output.info['LabelNames']: raise ValueError("Label %s not in scan labels" % label) index = output.info['LabelNames'].index(label) if output.x is None: output.x = [] output.x.append(output.data[:, index]) indexlist.append(index) npoints = output.x[0].shape[0] output.info['selection'] = selection output.info['selection']['x'] = indexlist for i in range(len(output.x)): output.x[i] = numpy.outer(output.x[i], ones).flatten() tmp = numpy.outer(channels, numpy.ones(float(npoints))).flatten() output.x.append(tmp) output.y = [numpy.zeros(nChannels * npoints,numpy.float64)] for i in range(npoints): mca_key = '%s.%d.%d' % (key, 1+detectorNumber, 1) mcaData = self._getMcaData(mca_key) output.y[0][(i*nChannels):((i+1)*nChannels)] = mcaData.data[:] if 'm' in selection: indexlist = [] for labelindex in selection['m']: if 'cntlist' in selection: label = selection['cntlist'][labelindex] else: label = output.info['LabelNames'][labelindex] if label not in output.info['LabelNames']: raise ValueError("Label %s not in scan labels" % label) index = output.info['LabelNames'].index(label) if output.m is None: output.m = [] output.m.append(output.data[:, index]) indexlist.append(index) output.info['selection']['m'] = indexlist if output.m is not None: output.m[0] = numpy.outer(output.m[0], ones).flatten() output.info['selection']['cntlist'] = output.info['LabelNames'] output.info['selectiontype'] = "3D" output.info['LabelNames'] = selection['cntlist'] + selection['mcalist'] output.data = None return output def _getScanData(self, scan_key, raw=False): index = 0 scan_obj = self._sourceObjectList[index].select(scan_key) scan_info= self.__getScanInfo(scan_key) scan_info["Key"] = scan_key scan_info["FileInfo"] = self.__getFileInfo() scan_type = scan_info["ScanType"] scan_data = None if scan_type&SF_SCAN: try: scan_data= numpy.transpose(scan_obj.data()).copy() except: raise IOError("SF_SCAN read failed") elif scan_type&SF_MESH: try: if raw: try: scan_data= numpy.transpose(scan_obj.data()).copy() except: raise IOError("SF_MESH read failed") else: scan_array = scan_obj.data() (mot1,mot2,cnts) = self.__getMeshSize(scan_array) scan_data = numpy.zeros((mot1,mot2,cnts), numpy.float64) for idx in range(mot2): scan_data[:,idx,:] = numpy.transpose(scan_array[:,idx*mot1:(idx+1)*mot1]).copy() scan_data = numpy.transpose(scan_data).copy() except: raise IOError("SF_MESH read failed") elif scan_type&SF_MCA: try: scan_data = scan_obj.mca(1) except: raise IOError("SF_MCA read failed") elif scan_type&SF_NMCA: try: scan_data = scan_obj.mca(1) except: raise IOError("SF_NMCA read failed") if scan_data is not None: #create data object dataObject = DataObject.DataObject() #data.info = self.__getKeyInfo(key) dataObject.info = scan_info dataObject.data = scan_data return dataObject else: raise TypeError("getData unknown type") def _getMcaData(self, key): index = 0 key_split= key.split(".") scan_key= key_split[0]+"."+key_split[1] scan_info = {} scan_info["Key"]= key scan_info["FileInfo"] = self.__getFileInfo() scan_obj = self._sourceObjectList[index].select(scan_key) scan_info.update(self.__getScanInfo(scan_key)) scan_type= scan_info["ScanType"] scan_data= None mca_range= [] # for each dim., (name, length, values or None) if len(key_split)==3: if scan_type&SF_NMCA or scan_type&SF_MCA: try: mca_no= int(key_split[2]) scan_data= scan_obj.mca(mca_no) except: raise IOError("Single MCA read failed") if scan_data is not None: scan_info.update(self.__getMcaInfo(mca_no, scan_obj, scan_info)) dataObject = DataObject.DataObject() dataObject.info = scan_info dataObject.data = scan_data return dataObject elif len(key_split) == 4: if scan_type == SF_SCAN + SF_NMCA: try: mca_no = (int(key_split[2])-1) * scan_info["NbMcaDet"] + \ int(key_split[3]) scan_data = scan_obj.mca(mca_no) except: raise IOError("SF_SCAN+SF_NMCA read failed") elif scan_type == SF_MESH + SF_MCA: try: #scan_array= scan_obj.data() #(mot1,mot2,cnts)= self.__getMeshSize(scan_array) #mca_no= 1 + int(key_split[2]) + int(key_split[3])*mot1 mca_no = (int(key_split[2])-1) * scan_info["NbMcaDet"] + \ int(key_split[3]) _logger.debug("try to read mca number = %s", mca_no) _logger.debug("total number of mca = %s", scan_info["NbMca"]) scan_data = scan_obj.mca(mca_no) except: raise IOError("SF_MESH+SF_MCA read failed") elif scan_type & SF_NMCA or scan_type & SF_MCA: try: mca_no = (int(key_split[2])-1) * scan_info["NbMcaDet"] + \ int(key_split[3]) scan_data = scan_obj.mca(mca_no) except: raise IOError("SF_MCA or SF_NMCA read failed") else: raise TypeError("Unknown scan type!!!!!!!!!!!!!!!!") if scan_data is not None: scan_info.update(self.__getMcaInfo(mca_no, scan_obj, scan_info)) dataObject = DataObject.DataObject() dataObject.info = scan_info dataObject.data = scan_data return dataObject def __getFileInfo(self): index = 0 source = self._sourceObjectList[index] file_info={} try: file_info["Title"] = source.title() except: file_info["Title"] = None try: file_info["User"] = source.user() except: file_info["User"] = None try: file_info["Date"] = source.date() except: file_info["Date"] = None try: file_info["Epoch"] = source.epoch() except: file_info["Epoch"] = None try: file_info["ScanNo"] = source.scanno() except: file_info["ScanNo"] = None return file_info def __getMeshSize(self, scan_array): """ Given the scandata array, return the size tuple of the mesh """ mot2_array = scan_array[1] mot2_max = mot2_array.shape[0] mot1_idx = 1 while mot1_idx < mot2_max and mot2_array[mot1_idx] == mot2_array[0]: mot1_idx+=1 mot2_idx = scan_array.shape[1] // mot1_idx cnts_idx = scan_array.shape[0] return (mot1_idx, mot2_idx, cnts_idx) def __getScanMotorRange(self, info, obj): name = info["LabelNames"][0] values = obj.datacol(1) length = values.shape[0] return (name, values, length) def __getMeshMotorRange(self, info, obj): return () def isUpdated(self, sourceName, key): #sourceName is redundant because only the first file is retained. index = 0 if not os.path.exists(self.__sourceNameList[index]): if _logger.getEffectiveLevel() == logging.DEBUG: t0 = time.time() # bliss case if self.__source_info_cached is None: return False sourcekeys = self.__source_info_cached['KeyList'] if key not in sourcekeys: return False if key != sourcekeys[-1]: # not the last key and only last scan is supposed to change return False # check the source might have changed respect to what is # available for this module key_info = self.__getScanInfo(key) npoints = key_info['Lines'] nmca = key_info["NbMca"] if (npoints > self.__source_info_cached["NumPts"][-1]) or \ (nmca > self.__source_info_cached["NumMca"][-1]): return True # the problem that remains is if there are new scans taken after the last # one was finished. That is supposed to be handled by the isUpdated method if present if hasattr(self._sourceObjectList[0], "isUpdated"): if self._sourceObjectList[0].isUpdated(): return True if _logger.getEffectiveLevel() == logging.DEBUG: _logger.debug("Update check took %s seconds", time.time() - t0) return False lastmodified = os.path.getmtime(self.__sourceNameList[index]) if key not in self.__lastKeyInfo.keys(): #nothing has been read??? self.__lastKeyInfo[key] = lastmodified return False if lastmodified != self.__lastKeyInfo[key]: # do not update the __lastKeyInfo because until # refresh is not called data will not be updated return True else: return False source_types = { SOURCE_TYPE: SpecFileDataSource} def DataSource(name="", source_type=SOURCE_TYPE): try: sourceClass = source_types[source_type] except KeyError: #ERROR invalid source type raise TypeError("Invalid Source Type, source type should be one of %s" % source_types.keys()) return sourceClass(name) if __name__ == "__main__": if len(sys.argv) not in [2,3,4]: print("Usage: %s []") sys.exit() filename= sys.argv[1] sf = SpecFileDataSource(filename) sf = DataSource(filename) if len(sys.argv)==2: import time for i in range(2): t0 = time.time() info = sf.getSourceInfo() print("getSourceInfo %d elapsed = " % i, time.time() - t0) print("Filename :", sf.sourceName) print("Number of scans :", info["Size"]) print("S# - command - pts - mca - type") for (s,c,p,m,t) in zip(info["KeyList"],info["Commands"],info["NumPts"],info["NumMca"],info["ScanType"]): print(s,"-",c,"-",p,"-",m,"-",t) print("KeyList = ",info["KeyList"]) if len(sys.argv)==3: t0 = time.time() dataObject = sf.getDataObject(sys.argv[2]) t0 = time.time() - t0 info= dataObject.info data= dataObject.data print("Filename :", info['SourceName']) print("Loaded key :", info["Key"]) print("Header :") for i,v in info.items(): print("-", i, ":", v) print("Data Shape :", data.shape) print("read time = ",t0) if len(sys.argv)==4: t0 = time.time() label = sys.argv[3] dataObject = sf.getDataObject(sys.argv[2], selection={'x':[label], 'y':[label], 'm':[label]}) t0 = time.time() - t0 info= dataObject.info #print dataObject.x print(dataObject.y) #print dataObject.x