1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894
|
#/*##########################################################################
#
# 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 <filename> [<key_to_load>]")
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
|