Source code for PyMca5.PyMcaCore.SpecFileDataSource

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__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
from . import DataObject
from PyMca5.PyMcaIO import specfilewrapper as specfile

SOURCE_TYPE = "SpecFile"
DEBUG = 0

# 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


[docs]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()
[docs] 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 = {}
[docs] 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 num_mca=[] num_pts=[] commands=[] sf_type=[] for i in scanlist: sel=self._sourceObjectList[0].select(i) if self.__fileHeaderList[0] == False: try: self.__fileHeaderList[0] = sel.fileheader('') except: 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["FileHeader"]=self.__fileHeaderList[0] source_info["NumMca"]=num_mca source_info["NumPts"]=num_pts source_info["Commands"]= commands source_info["ScanType"]= 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
[docs] 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) self.__lastKeyInfo[key] = os.path.getmtime(fileName) return self.__getScanInfo(scan_key)
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: 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: if DEBUG: print("Warning","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: if DEBUG: print("Warning","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: if DEBUG: print("Warning","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)
[docs] 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 if DEBUG: print("SELECTION = ", selection) print("key_type = ", 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.float)] output.y = [output.data[:].astype(numpy.float)] 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.float)] 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.float) 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]) if DEBUG: print("try to read mca number = ",mca_no) print("total number of mca = ",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 ()
[docs] def isUpdated(self, sourceName, key):
#sourceName is redundant? index = 0 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]: self.__lastKeyInfo[key] = lastmodified return True else: return False
source_types = { SOURCE_TYPE: SpecFileDataSource}
[docs]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__": import time if len(sys.argv) not in [2,3,4]: print("Usage: %s <filename> [<key_to_load>]") sys.exit() filename= sys.argv[1] sf = SpecFileDataSource(filename) sf = DataSource(filename) if len(sys.argv)==2: info= sf.getSourceInfo() 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"]) #print info['Channel0'] 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