#!/usr/bin/env python #/*########################################################################## # # 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 _logger = logging.getLogger(__name__) #the file format is based on XML import xml.etree.ElementTree as ElementTree from PyMca5.PyMcaCore import DataObject from PyMca5.PyMcaIO import ArtaxFileParser from PyMca5.PyMcaIO import SpecFileStack #SOURCE_TYPE = "EdfFileStack" SOURCE_TYPE ="SpecFileStack" myFloat = ArtaxFileParser.myFloat class RTXMap(DataObject.DataObject): ''' Class to read ARTAX .rtx files ''' def __init__(self, filename): ''' Parameters: ----------- filename : str Name of the .rtx file. ''' if not os.path.exists(filename): raise IOError("File %s does not exists" % filename) if 0: # this works but it is very slow DataObject.DataObject.__init__(self) stack = SpecFileStack.SpecFileStack(filename) self.data = stack.data self.info = stack.info return sf = ArtaxFileParser.ArtaxFileParser(filename) # get some Artax map specific information tScanInfo = sf.artaxTScanInfo # the rest is specfile like nScans = sf.scanno() scan = sf[0] calib0 = scan.header("@CALIB") ctime = scan.header("@CTIME") positioners = None motorNames = sf.allmotors() # assuming dictionaries are ordered if len(motorNames): positioners = {} for mne in motorNames: positioners[mne] = numpy.zeros((nScans,), dtype=numpy.float32) if ctime: liveTime = numpy.zeros((nScans,), dtype=numpy.float32) spectrum = sf[0].mca(1) data = numpy.zeros((1, nScans, len(spectrum)), dtype=numpy.float32) for i in range(nScans): scan = sf[i] if ctime: ctime = scan.header("@CTIME")[0] liveTime[i] = myFloat(ctime.split()[-2]) if positioners: motorPos = scan.allmotorpos() for mneIdx in range(len(motorNames)): mne = motorNames[mneIdx] positioners[mne][i] = motorPos[mneIdx] data[0, i] = scan.mca(1) DataObject.DataObject.__init__(self) self.data = data if positioners: self.info["positioners"] = positioners if ctime: self.info["McaLiveTime"] = liveTime self.info["McaCalib"] = [myFloat(x) for x in calib0[0].split()[1:]] self.info["SourceName"] = os.path.abspath(filename) if tScanInfo.get("Mapping", False): _logger.info("Regular Artax Map") else: _logger.info("Non-regular Artax Map") # we are supposed to have a regular map # let's figure out the shape? if tScanInfo["XFirst"] == tScanInfo["XLast"] and \ tScanInfo["YFirst"] != tScanInfo["YLast"] and \ tScanInfo["ZFirst"] != tScanInfo["ZLast"]: _logger.info("YZ scan if Y and Z are finite") meshType = "YZ" elif tScanInfo["XFirst"] != tScanInfo["XLast"] and \ tScanInfo["YFirst"] != tScanInfo["YLast"] and \ tScanInfo["ZFirst"] == tScanInfo["ZLast"]: _logger.info("XY scan if X and Y are finite") meshType = "XY" elif tScanInfo["XFirst"] != tScanInfo["XLast"] and \ tScanInfo["YFirst"] == tScanInfo["YLast"] and \ tScanInfo["ZFirst"] != tScanInfo["ZLast"]: _logger.info("XZ scan if X and Z are finite") meshType = "XZ" elif tScanInfo["XFirst"] != tScanInfo["XLast"] and \ tScanInfo["YFirst"] != tScanInfo["YLast"] and \ numpy.isnan(tScanInfo["ZFirst"]) and \ numpy.isnan(tScanInfo["ZLast"]): _logger.info("XY scan if X and Y are finite") meshType = "XY" else: meshType = None if meshType: for axis in meshType: key=axis+"First" if not numpy.isfinite(tScanInfo[key]): meshType = None break if meshType == "XY": _logger.info("XY scan") x = positioners["x"] y = positioners["y"] xFirst = tScanInfo["XFirst"] xLast = tScanInfo["XLast"] yFirst = tScanInfo["YFirst"] yLast = tScanInfo["YLast"] elif meshType == "XZ": _logger.info("XZ scan") x = positioners["x"] y = positioners["z"] xFirst = tScanInfo["XFirst"] xLast = tScanInfo["XLast"] yFirst = tScanInfo["ZFirst"] yLast = tScanInfo["ZLast"] elif meshType == "YZ": _logger.info("YZ scan") x = positioners["y"] y = positioners["z"] xFirst = tScanInfo["YFirst"] xLast = tScanInfo["YLast"] yFirst = tScanInfo["ZFirst"] yLast = tScanInfo["ZLast"] else: return if len(x) == 1 or len(y) == 1: return reasonableDeltaX = numpy.abs(x.max() - x.min()) / (1.0 + len(x)) reasonableDeltaY = numpy.abs(y.max() - y.min()) / (1.0 + len(y)) if numpy.abs(x[1] - x[0]) > reasonableDeltaX: x0 = x[0] i = 1 while (i < len(x)) and (numpy.abs(x[i] - x[0]) > reasonableDeltaX): i += 1 nColumns = i else: x0 = x[0] i = 0 while (i < len(x)) and (numpy.abs(x[i] - x[0]) < reasonableDeltaX): i += 1 nColumns = i # the scan can be in zig-zag # it is safer to rely on the scatter view if nScans % nColumns == 0: nRows = nScans // nColumns self.data.shape = nRows, nColumns, -1 self.info["xScale"] = [xFirst, (xLast - xFirst) / nColumns] self.info["yScale"] = [yFirst, (yLast - yFirst) / nRows] def isRTXMap(filename): try: if filename[-3:].lower() not in ["rtx", "spx"]: return False with open(filename, 'rb') as f: # expected to read an xml file someChar = f.read(20).decode() if "<" in someChar and "xml version" in someChar: return True except: pass return False def test(filename): print("isRTXMap? = ", isRTXMap(filename)) a = RTXMap(filename) print("info = ", a.info) print("Data shape = ", a.data.shape) if __name__ == "__main__": test(sys.argv[1])