#!/usr/bin/env python #/*########################################################################## # Copyright (C) 2004-2014 European Synchrotron Radiation Facility # # This file is part of the PyMca X-ray Fluorescence Toolkit developed at # the ESRF by the Software group. # # This toolkit is free software; you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by the Free # Software Foundation; either version 2 of the License, or (at your option) # any later version. # # PyMca is distributed in the hope that it will be useful, but WITHOUT ANY # WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU General Public License for more # details. # # You should have received a copy of the GNU General Public License along with # PyMca; if not, write to the Free Software Foundation, Inc., # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. # # PyMca follows the dual licensing model of Riverbank's PyQt and cannot be # used as a free plugin for a non-free program. # # Please contact the ESRF industrial unit (industry@esrf.fr) if this license # is a problem for you. #############################################################################*/ __revision__ = "$Revision: 4.12$" import sys import os import time import subprocess from PyMca import PyMcaQt as qt QTVERSION = qt.qVersion() if QTVERSION > '4.0.0': try: import h5py from PyMca import NexusDataSource from PyMca import QNexusWidget from PyMca import HDF5Selection HDF5SUPPORT = True except ImportError: HDF5SUPPORT = False else: HDF5SUPPORT = False from PyMca import ConfigDict from PyMca import McaAdvancedFitBatch from PyMca import EdfFileLayer from PyMca import SpecFileLayer from PyMca.PyMca_Icons import IconDict from PyMca import McaCustomEvent from PyMca import EdfFileSimpleViewer from PyMca import QtMcaAdvancedFitReport from PyMca import HtmlIndex from PyMca import PyMcaDirs from PyMca import PyMcaBatchBuildOutput ROIWIDTH = 100. DEBUG = 0 class McaBatchGUI(qt.QWidget): def __init__(self,parent=None,name="PyMca batch fitting",fl=None, filelist=None,config=None,outputdir=None, actions=0): if QTVERSION < '4.0.0': if fl is None: fl = qt.Qt.WDestructiveClose qt.QWidget.__init__(self,parent,name,fl) self.setIcon(qt.QPixmap(IconDict['gioconda16'])) self.setCaption(name) else: qt.QWidget.__init__(self, parent) self.setWindowTitle(name) self.setWindowIcon(qt.QIcon(qt.QPixmap(IconDict['gioconda16']))) self._layout = qt.QVBoxLayout(self) self._layout.setMargin(0) self._layout.setSpacing(0) self._edfSimpleViewer = None self._timer = None self._processList = [] self._selection = None self.__build(actions) if filelist is None: filelist = [] self.inputDir = None self.outputDir = None if outputdir is not None: if os.path.exists(outputdir): self.outputDir = outputdir else: qt.QMessageBox.information(self, "INFO", "Directory %s does not exists\nUsing %s"% (outputdir, self.outputDir)) self.configFile = None self.setFileList(filelist) self.setConfigFile(config) self.setOutputDir(self.outputDir) def __build(self,actions): self.__grid= qt.QWidget(self) self._layout.addWidget(self.__grid) #self.__grid.setGeometry(qt.QRect(30,30,288,156)) if QTVERSION < '4.0.0': grid = qt.QGridLayout(self.__grid,3,3,11,6) grid.setColStretch(0,0) grid.setColStretch(1,1) grid.setColStretch(2,0) else: grid = qt.QGridLayout(self.__grid) grid.setMargin(11) grid.setSpacing(6) #input list listrow = 0 listlabel = qt.QLabel(self.__grid) listlabel.setText("Input File list:") if QTVERSION < '4.0.0': listlabel.setAlignment(qt.QLabel.WordBreak | qt.QLabel.AlignVCenter) self.__listView = qt.QTextView(self.__grid) self.__listView.setMaximumHeight(30*listlabel.sizeHint().height()) else: self.__listView = qt.QTextEdit(self.__grid) self.__listView.setMaximumHeight(30*listlabel.sizeHint().height()) self.__listButton = qt.QPushButton(self.__grid) self.__listButton.setText('Browse') self.connect(self.__listButton,qt.SIGNAL('clicked()'),self.browseList) grid.addWidget(listlabel, listrow, 0, qt.Qt.AlignTop|qt.Qt.AlignLeft) grid.addWidget(self.__listView, listrow, 1) grid.addWidget(self.__listButton,listrow, 2, qt.Qt.AlignTop|qt.Qt.AlignRight) if HDF5SUPPORT: self._hdf5Widget = HDF5Selection.HDF5Selection(self) grid.addWidget(self._hdf5Widget, listrow+1, 0, 1, 3) row_offset = 1 self._hdf5Widget.hide() else: row_offset = 0 #config file configrow = 1 + row_offset configlabel = qt.QLabel(self.__grid) configlabel.setText("Fit Configuration File:") if QTVERSION < '4.0.0': configlabel.setAlignment(qt.QLabel.WordBreak | qt.QLabel.AlignVCenter) self.__configLine = qt.QLineEdit(self.__grid) self.__configLine.setReadOnly(True) self.__configButton = qt.QPushButton(self.__grid) self.__configButton.setText('Browse') self.connect(self.__configButton,qt.SIGNAL('clicked()'),self.browseConfig) grid.addWidget(configlabel, configrow, 0, qt.Qt.AlignLeft) grid.addWidget(self.__configLine, configrow, 1) grid.addWidget(self.__configButton, configrow, 2, qt.Qt.AlignLeft) #output dir outrow = 2 + row_offset outlabel = qt.QLabel(self.__grid) outlabel.setText("Output dir:") if QTVERSION < '4.0.0': outlabel.setAlignment(qt.QLabel.WordBreak | qt.QLabel.AlignVCenter) self.__outLine = qt.QLineEdit(self.__grid) self.__outLine.setReadOnly(True) #self.__outLine.setSizePolicy(qt.QSizePolicy(qt.QSizePolicy.Maximum, qt.QSizePolicy.Fixed)) self.__outButton = qt.QPushButton(self.__grid) self.__outButton.setText('Browse') self.connect(self.__outButton,qt.SIGNAL('clicked()'),self.browseOutputDir) grid.addWidget(outlabel, outrow, 0, qt.Qt.AlignLeft) grid.addWidget(self.__outLine, outrow, 1) grid.addWidget(self.__outButton, outrow, 2, qt.Qt.AlignLeft) box = qt.QWidget(self) box.l = qt.QHBoxLayout(box) box.l.setMargin(11) box.l.setSpacing(0) vbox1 = qt.QWidget(box) vbox1.l = qt.QVBoxLayout(vbox1) vbox1.l.setMargin(0) vbox1.l.setSpacing(0) box.l.addWidget(vbox1) vbox2 = qt.QWidget(box) vbox2.l = qt.QVBoxLayout(vbox2) vbox2.l.setMargin(0) vbox2.l.setSpacing(0) box.l.addWidget(vbox2) vbox3 = qt.QWidget(box) vbox3.l = qt.QVBoxLayout(vbox3) vbox3.l.setMargin(0) vbox3.l.setSpacing(0) box.l.addWidget(vbox3) self.__fitBox = qt.QCheckBox(vbox1) self.__fitBox.setText('Generate .fit Files') palette = self.__fitBox.palette() #if QTVERSION < '4.0.0': # palette.setDisabled(palette.active()) #else: # print("palette set disabled") self.__fitBox.setChecked(False) self.__fitBox.setEnabled(True) vbox1.l.addWidget(self.__fitBox) self.__imgBox = qt.QCheckBox(vbox2) self.__imgBox.setText('Generate Peak Images') palette = self.__imgBox.palette() if QTVERSION < '4.0.0': palette.setDisabled(palette.active()) else: if DEBUG: print("palette set disabled") self.__imgBox.setChecked(True) self.__imgBox.setEnabled(False) vbox2.l.addWidget(self.__imgBox) """ self.__specBox = qt.QCheckBox(box) self.__specBox.setText('Generate Peak Specfile') palette = self.__specBox.palette() palette.setDisabled(palette.active()) self.__specBox.setChecked(False) self.__specBox.setEnabled(False) """ self.__htmlBox = qt.QCheckBox(vbox3) self.__htmlBox.setText('Generate Report (SLOW!)') #palette = self.__htmlBox.palette() #palette.setDisabled(palette.active()) self.__htmlBox.setChecked(False) self.__htmlBox.setEnabled(True) vbox3.l.addWidget(self.__htmlBox) #report options #reportBox = qt.QHBox(self) self.__tableBox = qt.QCheckBox(vbox1) self.__tableBox.setText('Table in Report') palette = self.__tableBox.palette() #if QTVERSION < '4.0.0': # palette.setDisabled(palette.active()) #else: # print("palette set disabled") self.__tableBox.setChecked(True) self.__tableBox.setEnabled(False) vbox1.l.addWidget(self.__tableBox) self.__extendedTable = qt.QCheckBox(vbox2) self.__extendedTable.setText('Extended Table') self.__extendedTable.setChecked(True) self.__extendedTable.setEnabled(False) vbox2.l.addWidget(self.__extendedTable) self.__concentrationsBox = qt.QCheckBox(vbox3) self.__concentrationsBox.setText('Concentrations') self.__concentrationsBox.setChecked(False) self.__concentrationsBox.setEnabled(True) #self.__concentrationsBox.setEnabled(False) vbox3.l.addWidget(self.__concentrationsBox) self._layout.addWidget(box) # other stuff bigbox = qt.QWidget(self) bigbox.l = qt.QHBoxLayout(bigbox) bigbox.l.setMargin(0) bigbox.l.setSpacing(0) vBox = qt.QWidget(bigbox) vBox.l = qt.QVBoxLayout(vBox) vBox.l.setMargin(0) vBox.l.setSpacing(2) bigbox.l.addWidget(vBox) if 0: #These options are obsolete now self.__overwrite = qt.QCheckBox(vBox) self.__overwrite.setText('Overwrite Fit Files') self.__overwrite.setChecked(True) vBox.l.addWidget(self.__overwrite) self.__useExisting = qt.QCheckBox(vBox) self.__useExisting.setText('Use Existing Fit Files') self.__useExisting.setChecked(False) vBox.l.addWidget(self.__useExisting) self.connect(self.__overwrite, qt.SIGNAL("clicked()"), self.__clickSignal0) self.connect(self.__useExisting, qt.SIGNAL("clicked()"), self.__clickSignal1) self.connect(self.__concentrationsBox, qt.SIGNAL("clicked()"), self.__clickSignal2) self.connect(self.__htmlBox, qt.SIGNAL("clicked()"), self.__clickSignal3) boxStep0 = qt.QWidget(bigbox) boxStep0.l = qt.QVBoxLayout(boxStep0) boxStep = qt.QWidget(boxStep0) boxStep.l= qt.QHBoxLayout(boxStep) boxStep.l.setMargin(0) boxStep.l.setSpacing(0) boxStep0.l.addWidget(boxStep) bigbox.l.addWidget(boxStep0) if 0: self.__boxFStep = qt.QWidget(boxStep) boxFStep = self.__boxFStep boxFStep.l = qt.QHBoxLayout(boxFStep) boxFStep.l.setMargin(0) boxFStep.l.setSpacing(0) boxStep.l.addWidget(boxFStep) label= qt.QLabel(boxFStep) label.setText("File Step:") self.__fileSpin = qt.QSpinBox(boxFStep) if QTVERSION < '4.0.0': self.__fileSpin.setMinValue(1) self.__fileSpin.setMaxValue(10) else: self.__fileSpin.setMinimum(1) self.__fileSpin.setMaximum(10) self.__fileSpin.setValue(1) boxFStep.l.addWidget(label) boxFStep.l.addWidget(self.__fileSpin) self.__boxMStep = qt.QWidget(boxStep0) boxMStep = self.__boxMStep boxMStep.l = qt.QHBoxLayout(boxMStep) boxMStep.l.setMargin(0) boxMStep.l.setSpacing(0) boxStep0.l.addWidget(boxMStep) label= qt.QLabel(boxMStep) label.setText("MCA Step:") self.__mcaSpin = qt.QSpinBox(boxMStep) if QTVERSION < '4.0.0': self.__mcaSpin.setMinValue(1) self.__mcaSpin.setMaxValue(10) else: self.__mcaSpin.setMinimum(1) self.__mcaSpin.setMaximum(10) self.__mcaSpin.setValue(1) boxMStep.l.addWidget(label) boxMStep.l.addWidget(self.__mcaSpin) #box2 = qt.QHBox(self) self.__roiBox = qt.QCheckBox(vBox) self.__roiBox.setText('ROI Fitting Mode') vBox.l.addWidget(self.__roiBox) #box3 = qt.QHBox(box2) self.__box3 = qt.QWidget(boxStep0) box3 = self.__box3 box3.l = qt.QHBoxLayout(box3) box3.l.setMargin(0) box3.l.setSpacing(0) boxStep0.l.addWidget(box3) label= qt.QLabel(box3) label.setText("ROI Width (eV):") self.__roiSpin = qt.QSpinBox(box3) if QTVERSION < '4.0.0': self.__roiSpin.setMinValue(10) self.__roiSpin.setMaxValue(1000) else: self.__roiSpin.setMinimum(10) self.__roiSpin.setMaximum(1000) self.__roiSpin.setValue(ROIWIDTH) box3.l.addWidget(label) box3.l.addWidget(self.__roiSpin) #BATCH SPLITTING self.__splitBox = qt.QCheckBox(vBox) self.__splitBox.setText('EXPERIMENTAL: Use several processes') vBox.l.addWidget(self.__splitBox) #box3 = qt.QHBox(box2) self.__box4 = qt.QWidget(boxStep0) box4 = self.__box4 box4.l = qt.QHBoxLayout(box4) box4.l.setMargin(0) box4.l.setSpacing(0) boxStep0.l.addWidget(box4) label= qt.QLabel(box4) label.setText("Number of processes:") self.__splitSpin = qt.QSpinBox(box4) if QTVERSION < '4.0.0': self.__splitSpin.setMinValue(1) self.__splitSpin.setMaxValue(1000) else: self.__splitSpin.setMinimum(1) self.__splitSpin.setMaximum(1000) self.__splitSpin.setValue(2) box4.l.addWidget(label) box4.l.addWidget(self.__splitSpin) self._layout.addWidget(bigbox) if actions: self.__buildActions() def __clickSignal0(self): if self.__overwrite.isChecked(): self.__useExisting.setChecked(0) else: self.__useExisting.setChecked(1) def __clickSignal1(self): if self.__useExisting.isChecked(): self.__overwrite.setChecked(0) else: self.__overwrite.setChecked(1) def __clickSignal2(self): #self.__tableBox.setEnabled(True) pass def __clickSignal3(self): if self.__htmlBox.isChecked(): self.__tableBox.setEnabled(True) #self.__concentrationsBox.setEnabled(True) self.__fitBox.setChecked(True) self.__fitBox.setEnabled(False) else: self.__tableBox.setEnabled(False) #self.__concentrationsBox.setEnabled(False) self.__fitBox.setChecked(False) self.__fitBox.setEnabled(True) def __buildActions(self): box = qt.QWidget(self) box.l = qt.QHBoxLayout(box) box.l.addWidget(qt.HorizontalSpacer(box)) self.__dismissButton = qt.QPushButton(box) box.l.addWidget(self.__dismissButton) box.l.addWidget(qt.HorizontalSpacer(box)) self.__dismissButton.setText("Close") self.__startButton = qt.QPushButton(box) box.l.addWidget(self.__startButton) box.l.addWidget(qt.HorizontalSpacer(box)) self.__startButton.setText("Start") self.connect(self.__dismissButton,qt.SIGNAL("clicked()"),self.close) self.connect(self.__startButton,qt.SIGNAL("clicked()"),self.start) self._layout.addWidget(box) def close(self): if self._edfSimpleViewer is not None: self._edfSimpleViewer.close() self._edfSimpleViewer = None qt.QWidget.close(self) def setFileList(self,filelist=None): if filelist is None:filelist = [] if True or self.__goodFileList(filelist): text = "" oldtype = None #do not sort the file list #respect user choice #filelist.sort() for file in filelist: filetype = self.__getFileType(file) if filetype is None:return if oldtype is None: oldtype = filetype if oldtype != filetype: qt.QMessageBox.critical(self, "ERROR", "Type %s does not match type %s on\n%s"% (filetype,oldtype,file)) return text += "%s\n" % file if len(filelist): if HDF5SUPPORT: if not h5py.is_hdf5(filelist[0]): self._hdf5Widget.hide() self._selection=None else: dialog = qt.QDialog(self) dialog.setWindowTitle('Select your data set') dialog.mainLayout = qt.QVBoxLayout(dialog) dialog.mainLayout.setMargin(0) dialog.mainLayout.setSpacing(0) datasource = NexusDataSource.NexusDataSource(filelist[0]) nexusWidget = QNexusWidget.QNexusWidget(dialog) nexusWidget.buttons.hide() nexusWidget.setDataSource(datasource) button = qt.QPushButton(dialog) button.setText("Done") button.setAutoDefault(True) qt.QObject.connect(button, qt.SIGNAL('clicked()'), dialog.accept) dialog.mainLayout.addWidget(nexusWidget) dialog.mainLayout.addWidget(button) ret = dialog.exec_() cntSelection = nexusWidget.cntTable.getCounterSelection() cntlist = cntSelection['cntlist'] if not len(cntlist): text = "No dataset selection" self.showMessage(text) self.__listView.clear() return if not len(cntSelection['y']): text = "No dataset selected as y" self.showMessage(text) self.__listView.clear() return datasource = None selection = {} selection['x'] = [] selection['y'] = [] selection['m'] = [] for key in ['x', 'y', 'm']: if len(cntSelection[key]): for idx in cntSelection[key]: selection[key].append(cntlist[idx]) self._selection = selection self._hdf5Widget.setSelection(selection) #they are not used yet #self._hdf5Widget.selectionWidgetsDict['x'].hide() #self._hdf5Widget.selectionWidgetsDict['m'].hide() if self._hdf5Widget.isHidden(): self._hdf5Widget.show() elif filelist[0][-3:].lower() in ['.h5', 'nxs', 'hdf']: text = "Warning, this looks as an HDF5 file " text += "but you do not have HDF5 support." self.showMessage(text) self.fileList = filelist if len(self.fileList): self.inputDir = os.path.dirname(self.fileList[0]) PyMcaDirs.inputDir = os.path.dirname(self.fileList[0]) if QTVERSION < '4.0.0': self.__listView.setText(text) else: self.__listView.clear() self.__listView.insertPlainText(text) def showMessage(self, text): msg = qt.QMessageBox(self) msg.setWindowTitle("PyMcaBatch Message") msg.setIcon(qt.QMessageBox.Information) msg.setText(text) msg.exec_() def setConfigFile(self,configfile=None): if configfile is None:return if self.__goodConfigFile(configfile): self.configFile = configfile if type(configfile) == type([]): #do not sort file list #self.configFile.sort() self.__configLine.setText(self.configFile[0]) self.lastInputDir = os.path.dirname(self.configFile[0]) else: self.__configLine.setText(configfile) self.lastInputDir = os.path.dirname(self.configFile) def setOutputDir(self,outputdir=None): if outputdir is None: return if self.__goodOutputDir(outputdir): self.outputDir = outputdir PyMcaDirs.outputDir = outputdir self.__outLine.setText(outputdir) else: qt.QMessageBox.critical(self, "ERROR", "Cannot use output directory:\n%s"% (outputdir)) def __goodFileList(self,filelist): if not len(filelist): return True for ffile in filelist: if not os.path.exists(ffile): qt.QMessageBox.critical(self, "ERROR", 'File %s\ndoes not exists' % ffile) if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() return False return True def __goodConfigFile(self,configfile0): if type(configfile0) != type([]): configfileList = [configfile0] else: configfileList = configfile0 for configfile in configfileList: if not os.path.exists(configfile): qt.QMessageBox.critical(self, "ERROR",'File %s\ndoes not exists' % configfile) if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() return False elif len(configfile.split()) > 1: if sys.platform != 'win32': qt.QMessageBox.critical(self, "ERROR",'Configuration File:\n %s\ncontains spaces in the path' % configfile) if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() return False return True def __goodOutputDir(self,outputdir): if not os.path.isdir(outputdir): return False elif len(outputdir.split()) > 1: if sys.platform != 'win32': qt.QMessageBox.critical(self, "ERROR", 'Output Directory:\n %s\ncontains spaces in the path' % outputdir) if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() return False return True def __getFileType(self,inputfile): try: ffile = None try: ffile = EdfFileLayer.EdfFileLayer(fastedf=0) ffile.SetSource(inputfile) fileinfo = ffile.GetSourceInfo() if fileinfo['KeyList'] == []:ffile=None return "EdfFile" except: pass if (ffile is None): ffile = SpecFileLayer.SpecFileLayer() ffile.SetSource(inputfile) del ffile return "Specfile" except: qt.QMessageBox.critical(self, sys.exc_info()[0], 'I do not know what to do with file\n %s' % ffile) if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() return None def browseList(self): self.inputDir = PyMcaDirs.inputDir if not os.path.exists(self.inputDir): self.inputDir = os.getcwd() wdir = self.inputDir if QTVERSION < '4.0.0': filedialog = qt.QFileDialog(self,"Open a set of files",1) filedialog.setMode(filedialog.ExistingFiles) filedialog.setDir(wdir) else: filedialog = qt.QFileDialog(self) filedialog.setWindowTitle("Open a set of files") filedialog.setDirectory(wdir) filedialog.setModal(1) filedialog.setFileMode(filedialog.ExistingFiles) filetypes = "McaFiles (*.mca)\nEdfFiles (*.edf)\n" if HDF5SUPPORT: filetypes += "HDF5 (*.nxs *.h5 *.hdf)\n" filetypes += "SpecFiles (*.spec)\nSpecFiles (*.dat)\nAll files (*)" #if (QTVERSION < '4.3.0') and sys.platform == "win32": if False and PyMcaDirs.nativeFileDialogs: #windows file dialogs have difficulties when dealing with #thousands of files, I do not know if other platforms too if QTVERSION < '4.0.0': filelist= filedialog.getOpenFileNames(qt.QString(filetypes), wdir, self,"openFile", "Open a set of files") else: filelist = qt.QFileDialog.getOpenFileNames(self, "Open a set of files", wdir, filetypes, None) #This should be the last file filter used else: if QTVERSION < '4.0.0': filedialog.setFilters(filetypes) ret = filedialog.exec_loop() else: filedialog.setFilters(filetypes.split("\n")) ret = filedialog.exec_() if ret == qt.QDialog.Accepted: filelist=filedialog.selectedFiles() else: if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() return if len(filelist): filelist = [qt.safe_str(x) for x in filelist] self.setFileList(filelist) if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() def browseConfig(self): self.inputDir = PyMcaDirs.inputDir if not os.path.exists(self.inputDir): self.inputDir = os.getcwd() wdir = self.inputDir if QTVERSION < '4.0.0': filename = qt.QFileDialog(self,"Open a new fit config file",1) filename.setMode(filename.ExistingFiles) filename.setDir(wdir) else: filename = qt.QFileDialog(self) filename.setWindowTitle("Open a new fit config file") filename.setModal(1) filename.setFileMode(filename.ExistingFiles) filename.setDirectory(wdir) filetypes = "Config Files (*.cfg)\nAll files (*)" if PyMcaDirs.nativeFileDialogs: if QTVERSION < '4.0.0': filenameList= filename.getOpenFileNames(qt.QString(filetypes), wdir, self,"openFile", "Open a new fit config file") else: filenameList = qt.QFileDialog.getOpenFileNames(self, "Open a new fit config file", wdir, filetypes, None) #This should be the filter used else: if QTVERSION < '4.0.0': filename.setFilters(filetypes) ret = filename.exec_loop() else: filename.setFilters(["Config Files (*.cfg)", "All files (*)"]) ret = filename.exec_() if ret == qt.QDialog.Accepted: filenameList = filename.selectedFiles() else: if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() return filename = [] for f in filenameList: filename.append(qt.safe_str(f)) if len(filename) == 1: self.setConfigFile(qt.safe_str(filename[0])) elif len(filenameList): self.setConfigFile(filename) if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() def browseOutputDir(self): self.outputDir = PyMcaDirs.outputDir if not os.path.exists(self.outputDir): self.outputDir = os.getcwd() wdir = self.outputDir if QTVERSION < '4.0.0': outfile = qt.QFileDialog(self,"Output Directory Selection",1) outfile.setMode(outfile.DirectoryOnly) outfile.setDir(wdir) ret = outfile.exec_loop() else: outfile = qt.QFileDialog(self) outfile.setWindowTitle("Output Directory Selection") outfile.setModal(1) outfile.setDirectory(wdir) outfile.setFileMode(outfile.DirectoryOnly) ret = outfile.exec_() if ret: if QTVERSION < '4.0.0': outdir=qt.safe_str(outfile.selectedFile()) else: outdir=qt.safe_str(outfile.selectedFiles()[0]) outfile.close() del outfile self.setOutputDir(outdir) else: outfile.close() del outfile if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() def start(self): if not len(self.fileList): qt.QMessageBox.critical(self, "ERROR",'Empty file list') if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() return if self.__splitBox.isChecked(): if sys.platform == 'darwin': if ".app" in os.path.dirname(__file__): text = 'Multiple processes only supported on MacOS X when built from source\n' text += 'and not when running the frozen binary.' qt.QMessageBox.critical(self, "ERROR",text) if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() return if len(self.fileList) == 1: if int(qt.safe_str(self.__splitSpin.text())) > 1: allowSingleFileSplitProcesses = False if HDF5SUPPORT: if h5py.is_hdf5(self.fileList[0]): if DEBUG: print("Disallow single HDF5 process split") print("due to problems with concurrent access") #allowSingleFileSplitProcesses = True allowSingleFileSplitProcesses = False if not allowSingleFileSplitProcesses: text = "Multiple processes can only be used with multiple input files." qt.QMessageBox.critical(self, "ERROR",text) if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() return if (self.configFile is None) or (not self.__goodConfigFile(self.configFile)): qt.QMessageBox.critical(self, "ERROR",'Invalid fit configuration file') if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() return if type(self.configFile) == type([]): if len(self.configFile) != len(self.fileList): qt.QMessageBox.critical(self, "ERROR", 'Number of config files should be either one or equal to number of files') if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() return if (self.outputDir is None) or (not self.__goodOutputDir(self.outputDir)): qt.QMessageBox.critical(self, "ERROR",'Invalid output directory') if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() return name = "Batch from %s to %s " % (os.path.basename(self.fileList[ 0]), os.path.basename(self.fileList[-1])) roifit = self.__roiBox.isChecked() html = self.__htmlBox.isChecked() #if html: concentrations = self.__concentrationsBox.isChecked() #else: # concentrations = 0 if self.__tableBox.isChecked(): if self.__extendedTable.isChecked(): table = 2 else: table = 1 else: table =0 #htmlindex = qt.safe_str(self.__htmlIndex.text()) htmlindex = "index.html" if html: if len(htmlindex)<5: htmlindex+=".html" if len(htmlindex) == 5: htmlindex = "index.html" if htmlindex[-5:] != "html": htmlindex+=".html" roiwidth = float(qt.safe_str(self.__roiSpin.text())) if 0: overwrite= self.__overwrite.isChecked() filestep = int(qt.safe_str(self.__fileSpin.text())) mcastep = int(qt.safe_str(self.__mcaSpin.text())) else: overwrite= 1 filestep = 1 mcastep = 1 if len(self.fileList) == 1: if self.__splitBox.isChecked(): nbatches = int(qt.safe_str(self.__splitSpin.text())) mcastep = nbatches fitfiles = self.__fitBox.isChecked() selection = self._selection if selection is None: selectionFlag = False else: selectionFlag = True if self._edfSimpleViewer is not None: self._edfSimpleViewer.close() self._edfSimpleViewer = None if roifit: window = McaBatchWindow(name="ROI"+name,actions=1, outputdir=self.outputDir, html=html, htmlindex=htmlindex, table = 0) b = McaBatch(window,self.configFile,self.fileList,self.outputDir,roifit=roifit, roiwidth=roiwidth,overwrite=overwrite,filestep=1,mcastep=1, concentrations=0, fitfiles=fitfiles, selection=selection) def cleanup(): b.pleasePause = 0 b.pleaseBreak = 1 b.wait() qt.qApp.processEvents() def pause(): if b.pleasePause: b.pleasePause=0 window.pauseButton.setText("Pause") else: b.pleasePause=1 window.pauseButton.setText("Continue") qt.QObject.connect(window.pauseButton,qt.SIGNAL("clicked()"),pause) qt.QObject.connect(window.abortButton,qt.SIGNAL("clicked()"),window.close) qt.QObject.connect(qt.qApp,qt.SIGNAL("aboutToQuit()"),cleanup) self.__window = window self.__b = b window.show() b.start() elif (sys.platform == 'darwin') and\ ((".app" in os.path.dirname(__file__)) or (not self.__splitBox.isChecked())): #almost identical to batch window = McaBatchWindow(name="ROI"+name,actions=1,outputdir=self.outputDir, html=html,htmlindex=htmlindex, table = table) b = McaBatch(window,self.configFile,self.fileList,self.outputDir,roifit=roifit, roiwidth=roiwidth,overwrite=overwrite,filestep=filestep, mcastep=mcastep, concentrations=concentrations, fitfiles=fitfiles, selection=selection) def cleanup(): b.pleasePause = 0 b.pleaseBreak = 1 b.wait() qt.qApp.processEvents() def pause(): if b.pleasePause: b.pleasePause=0 window.pauseButton.setText("Pause") else: b.pleasePause=1 window.pauseButton.setText("Continue") qt.QObject.connect(window.pauseButton,qt.SIGNAL("clicked()"),pause) qt.QObject.connect(window.abortButton,qt.SIGNAL("clicked()"),window.close) qt.QObject.connect(qt.qApp,qt.SIGNAL("aboutToQuit()"),cleanup) window._rootname = "%s"% b._rootname self.__window = window self.__b = b window.show() b.start() elif sys.platform == 'win32': listfile = os.path.join(self.outputDir, "tmpfile") self.genListFile(listfile, config=False) dirname = os.path.dirname(McaAdvancedFitBatch.__file__) tmpDirname = os.path.dirname(dirname) if tmpDirname.lower().endswith("exe") or\ tmpDirname.lower().endswith(".zip"): frozen = True dirname = os.path.dirname(tmpDirname) myself = os.path.join(dirname, "PyMcaBatch.exe") viewer = os.path.join(dirname, "EdfFileSimpleViewer.exe") rgb = os.path.join(dirname, "PyMcaPostBatch.exe") if not os.path.exists(viewer): viewer = None if not os.path.exists(rgb): rgb = None else: frozen = False myself = os.path.join(dirname, "PyMcaBatch.py") if not os.path.exists(myself): dirname = os.path.dirname(McaAdvancedFitBatch.__file__) myself = os.path.join(dirname, "PyMcaBatch.py") viewer = os.path.join(dirname, "EdfFileSimpleViewer.py") rgb = os.path.join(dirname, "PyMcaPostBatch.py") if not os.path.exists(viewer): viewer = None else: viewer = '%s "%s"' % (sys.executable, viewer) if not os.path.exists(rgb): rgb = None else: rgb = '%s "%s"' % (sys.executable, rgb) self._rgb = rgb if type(self.configFile) == type([]): cfglistfile = os.path.join(self.outputDir, "tmpfile.cfg") self.genListFile(cfglistfile, config=True) dirname = os.path.dirname(dirname) if frozen: cmd = '"%s" --cfglistfile="%s" --outdir="%s" --overwrite=%d --filestep=%d --mcastep=%d --html=%d --htmlindex=%s --listfile="%s" --concentrations=%d --table=%d --fitfiles=%d --selection=%d' %\ (myself, cfglistfile, self.outputDir, overwrite, filestep, mcastep, html,htmlindex, listfile,concentrations, table, fitfiles, selectionFlag) else: cmd = '%s "%s" --cfglistfile="%s" --outdir="%s" --overwrite=%d --filestep=%d --mcastep=%d --html=%d --htmlindex=%s --listfile="%s" --concentrations=%d --table=%d --fitfiles=%d --selection=%d' %\ (sys.executable,myself, cfglistfile, self.outputDir, overwrite, filestep, mcastep, html,htmlindex, listfile,concentrations, table, fitfiles, selectionFlag) else: if not frozen: cmd = '%s "%s" --cfg="%s" --outdir="%s" --overwrite=%d --filestep=%d --mcastep=%d --html=%d --htmlindex=%s --listfile="%s" --concentrations=%d --table=%d --fitfiles=%d --selection=%d' % \ (sys.executable, myself, self.configFile, self.outputDir, overwrite, filestep, mcastep, html,htmlindex, listfile,concentrations, table, fitfiles, selectionFlag) else: cmd = '"%s" --cfg="%s" --outdir="%s" --overwrite=%d --filestep=%d --mcastep=%d --html=%d --htmlindex=%s --listfile="%s" --concentrations=%d --table=%d --fitfiles=%d --selection=%d' % \ (myself, self.configFile, self.outputDir, overwrite, filestep, mcastep, html,htmlindex, listfile,concentrations, table, fitfiles, selectionFlag) self.hide() qt.qApp.processEvents() if DEBUG: print("cmd = %s" % cmd) if self.__splitBox.isChecked(): nbatches = int(qt.safe_str(self.__splitSpin.text())) if len(self.fileList) > 1: filechunk = int(len(self.fileList)/nbatches) processList = [] for i in range(nbatches): beginoffset = filechunk * i endoffset = len(self.fileList) - filechunk * (i+1) if (i+1) == nbatches:endoffset = 0 cmd1 = cmd + " --filebeginoffset=%d --fileendoffset=%d --chunk=%d" % \ (beginoffset, endoffset, i) try: processList.append(subprocess.Popen(cmd1, cwd=os.getcwd())) except UnicodeEncodeError: processList.append(\ subprocess.Popen(cmd1.encode(sys.getfilesystemencoding()), cwd=os.getcwd())) if DEBUG: print("cmd = %s" % cmd1) else: #f = open("CMD", 'wb') processList = [] for i in range(nbatches): #the mcastep has been dealt with above cmd1 = cmd + " --mcaoffset=%d --chunk=%d" % (i, i) processList.append(subprocess.Popen(cmd1, cwd=os.getcwd())) if DEBUG: print("CMD = %s" % cmd1) #f.write(cmd1+"\n") #f.close() self._processList = processList if self._timer is None: self._timer = qt.QTimer(self) qt.QObject.connect(self._timer, qt.SIGNAL('timeout()'), self._pollProcessList) if not self._timer.isActive(): self._timer.start(1000) else: print("timer was already active") return else: try: subprocess.call(cmd) except UnicodeEncodeError: try: subprocess.call(cmd.encode(sys.getfilesystemencoding())) except: # be ready for any weird error like missing that encoding try: subprocess.call(cmd.encode('utf-8')) except UnicodeEncodeError: subprocess.call(cmd.encode('latin-1')) self.show() else: listfile = os.path.join(self.outputDir, "tmpfile") self.genListFile(listfile, config=False) dirname = os.path.dirname(McaAdvancedFitBatch.__file__) tmpDirname = os.path.dirname(dirname) if tmpDirname.lower().endswith("exe") or\ tmpDirname.lower().endswith(".zip"): frozen = True dirname = os.path.dirname(tmpDirname) myself = os.path.join(dirname, "PyMcaBatch") viewer = os.path.join(dirname, "EdfFileSimpleViewer") rgb = os.path.join(dirname, "PyMcaPostBatch") if not os.path.exists(viewer): viewer = None if not os.path.exists(rgb): rgb = None else: myself = os.path.join(dirname, "PyMcaBatch.py") if not os.path.exists(os.path.join(dirname, myself)): dirname = os.path.dirname(McaAdvancedFitBatch.__file__) if not os.path.exists(os.path.join(dirname, myself)): text = 'Cannot locate PyMcaBatch.py file.\n' qt.QMessageBox.critical(self, "ERROR",text) if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() return myself = sys.executable+" "+ os.path.join(dirname, myself) viewer = os.path.join(dirname, "EdfFileSimpleViewer.py") rgb = os.path.join(dirname, "PyMcaPostBatch.py") if not os.path.exists(viewer): viewer = None else: viewer = '%s "%s"' % (sys.executable, viewer) if not os.path.exists(rgb): rgb = None else: rgb = '%s "%s"' % (sys.executable, rgb) self._rgb = rgb if type(self.configFile) == type([]): cfglistfile = os.path.join(self.outputDir, "tmpfile.cfg") self.genListFile(cfglistfile, config=True) cmd = "%s --cfglistfile=%s --outdir=%s --overwrite=%d --filestep=%d --mcastep=%d --html=%d --htmlindex=%s --listfile=%s --concentrations=%d --table=%d --fitfiles=%d --selection=%d &" % \ (myself, cfglistfile, self.outputDir, overwrite, filestep, mcastep, html, htmlindex, listfile, concentrations, table, fitfiles, selectionFlag) else: cmd = "%s --cfg=%s --outdir=%s --overwrite=%d --filestep=%d --mcastep=%d --html=%d --htmlindex=%s --listfile=%s --concentrations=%d --table=%d --fitfiles=%d --selection=%d &" % \ (myself, self.configFile, self.outputDir, overwrite, filestep, mcastep, html, htmlindex, listfile, concentrations, table, fitfiles, selectionFlag) if DEBUG: print("cmd = %s" % cmd) if self.__splitBox.isChecked(): qt.qApp.processEvents() nbatches = int(qt.safe_str(self.__splitSpin.text())) filechunk = int(len(self.fileList)/nbatches) processList = [] for i in range(nbatches): beginoffset = filechunk * i endoffset = len(self.fileList) - filechunk * (i+1) if (i+1) == nbatches:endoffset = 0 cmd1 = cmd.replace("&", "") + \ " --filebeginoffset=%d --fileendoffset=%d --chunk=%d" % \ (beginoffset, endoffset, i) # unfortunately I have to set shell = True # otherways I get a file not found error in the # chold process processList.append(\ subprocess.Popen(cmd1, cwd=os.getcwd(), shell=True, close_fds=True)) self._processList = processList self.hide() self._pollProcessList() if self._timer is None: self._timer = qt.QTimer(self) qt.QObject.connect(self._timer, qt.SIGNAL('timeout()'), self._pollProcessList) if not self._timer.isActive(): self._timer.start(1000) else: print("timer was already active") return else: os.system(cmd) msg = qt.QMessageBox(self) msg.setIcon(qt.QMessageBox.Information) text = "Your batch has been started as an independent process." msg.setText(text) if QTVERSION < '4.0.0': msg.exec_loop() else: msg.exec_() def genListFile(self, listfile, config=None): if os.path.exists(listfile): try: os.remove(listfile) except: print("Cannot delete file %s" % listfile) raise if config is None: lst = self.fileList elif config: lst = self.configFile else: lst = self.fileList if lst == self.fileList: if self._selection is not None: ddict = ConfigDict.ConfigDict() ddict['PyMcaBatch'] = {} ddict['PyMcaBatch']['filelist'] = lst ddict['PyMcaBatch']['selection'] = self._selection ddict.write(listfile) return fd=open(listfile, 'wb') for filename in lst: # only the file system encoding makes sense here fd.write(('%s\n' % filename).encode(sys.getfilesystemencoding())) fd.close() def _pollProcessList(self): processList = self._processList rgb = self._rgb if QTVERSION < '4.0.0':rgb = None n = 0 for process in processList: if process.poll() is None: n += 1 if n > 0: return self._timer.stop() self.show() if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() work = PyMcaBatchBuildOutput.PyMcaBatchBuildOutput(os.path.join(self.outputDir, "IMAGES")) if DEBUG: a, b, c = work.buildOutput(delete=False) else: a, b, c = work.buildOutput(delete=True) if len(a): if self._edfSimpleViewer is None: self._edfSimpleViewer = EdfFileSimpleViewer.EdfFileSimpleViewer() self._edfSimpleViewer.setFileList(a) self._edfSimpleViewer.show() if rgb is not None: if len(b): if sys.platform == "win32": try: subprocess.Popen('%s "%s"' % (rgb, b[0]), cwd = os.getcwd()) except UnicodeEncodeError: subprocess.Popen(('%s "%s"' % (rgb, b[0])).encode(sys.getfilesystemencoding()), cwd = os.getcwd()) else: os.system("%s %s &" % (rgb, b[0])) work = PyMcaBatchBuildOutput.PyMcaBatchBuildOutput(self.outputDir) if DEBUG: work.buildOutput(delete=False) else: work.buildOutput(delete=True) class McaBatch(qt.QThread,McaAdvancedFitBatch.McaAdvancedFitBatch): def __init__(self, parent, configfile, filelist=None, outputdir = None, roifit = None, roiwidth=None, overwrite=1, filestep=1, mcastep=1, concentrations=0, fitfiles=0, filebeginoffset=0, fileendoffset=0, mcaoffset=0, chunk=None, selection=None, lock=None): McaAdvancedFitBatch.McaAdvancedFitBatch.__init__(self, configfile, filelist, outputdir, roifit=roifit, roiwidth=roiwidth, overwrite=overwrite, filestep=filestep, mcastep=mcastep, concentrations=concentrations, fitfiles=fitfiles, filebeginoffset = filebeginoffset, fileendoffset = fileendoffset, mcaoffset = mcaoffset, chunk=chunk, selection=selection, lock=lock) qt.QThread.__init__(self) self.parent = parent self.pleasePause = 0 def run(self): self.processList() def onNewFile(self, ffile, filelist): self.__lastOnNewFile = ffile ddict = {'file':ffile, 'filelist':filelist, 'filestep':self.fileStep, 'filebeginoffset':self.fileBeginOffset, 'fileendoffset':self.fileEndOffset, 'event':'onNewFile'} if QTVERSION < '4.0.0': self.postEvent(self.parent, McaCustomEvent.McaCustomEvent(ddict)) else: qt.QApplication.postEvent(self.parent, McaCustomEvent.McaCustomEvent(ddict)) if self.pleasePause:self.__pauseMethod() def onImage(self, key, keylist): ddict = {'key':key, 'keylist':keylist, 'event':'onImage'} if QTVERSION < '4.0.0': self.postEvent(self.parent, McaCustomEvent.McaCustomEvent(ddict)) else: qt.QApplication.postEvent(self.parent, McaCustomEvent.McaCustomEvent(ddict)) def onMca(self, mca, nmca, filename=None, key=None, info=None): if DEBUG: print("onMca key = %s" % key) ddict = {'mca':mca, 'nmca':nmca, 'mcastep':self.mcaStep, 'filename':filename, 'key':key, 'info':info, 'outputdir':self._outputdir, 'useExistingFiles':self.useExistingFiles, 'roifit':self.roiFit, 'event':'onMca'} if QTVERSION < '4.0.0': self.postEvent(self.parent, McaCustomEvent.McaCustomEvent(ddict)) else: qt.QApplication.postEvent(self.parent, McaCustomEvent.McaCustomEvent(ddict)) if self.pleasePause:self.__pauseMethod() def onEnd(self): if DEBUG: print("onEnd") ddict = {'event':'onEnd', 'filestep':self.fileStep, 'mcastep':self.mcaStep, 'chunk':self.chunk, 'savedimages':self.savedImages} if QTVERSION < '4.0.0': self.postEvent(self.parent, McaCustomEvent.McaCustomEvent(ddict)) else: qt.QApplication.postEvent(self.parent, McaCustomEvent.McaCustomEvent(ddict)) if self.pleasePause: self.__pauseMethod() def __pauseMethod(self): if QTVERSION < '4.0.0': self.postEvent(self.parent, McaCustomEvent.McaCustomEvent({'event':'batchPaused'})) else: qt.QApplication.postEvent(self.parent, McaCustomEvent.McaCustomEvent({'event':'batchPaused'})) while(self.pleasePause): time.sleep(1) if QTVERSION < '4.0.0': self.postEvent(self.parent, McaCustomEvent.McaCustomEvent({'event':'batchResumed'})) else: qt.QApplication.postEvent(self.parent, McaCustomEvent.McaCustomEvent({'event':'batchResumed'})) class McaBatchWindow(qt.QWidget): def __init__(self,parent=None, name="BatchWindow", fl=0, actions = 0, outputdir=None, html=0, htmlindex = None, table=2, chunk = None): if QTVERSION < '4.0.0': qt.QWidget.__init__(self, parent, name, fl) self.setCaption(name) else: qt.QWidget.__init__(self, parent) self.setWindowTitle(name) self.chunk = chunk self.l = qt.QVBoxLayout(self) #self.l.setAutoAdd(1) self.bars =qt.QWidget(self) self.l.addWidget(self.bars) if QTVERSION < '4.0.0': self.barsLayout = qt.QGridLayout(self.bars,2,3) else: self.barsLayout = qt.QGridLayout(self.bars) self.barsLayout.setMargin(2) self.barsLayout.setSpacing(3) self.progressBar = qt.QProgressBar(self.bars) self.progressLabel = qt.QLabel(self.bars) self.progressLabel.setText('File Progress:') self.imageBar = qt.QProgressBar(self.bars) self.imageLabel = qt.QLabel(self.bars) self.imageLabel.setText('Image in File:') self.mcaBar = qt.QProgressBar(self.bars) self.mcaLabel = qt.QLabel(self.bars) self.mcaLabel.setText('MCA in Image:') self.barsLayout.addWidget(self.progressLabel,0,0) self.barsLayout.addWidget(self.progressBar,0,1) self.barsLayout.addWidget(self.imageLabel,1,0) self.barsLayout.addWidget(self.imageBar,1,1) self.barsLayout.addWidget(self.mcaLabel,2,0) self.barsLayout.addWidget(self.mcaBar,2,1) self.status = qt.QLabel(self) self.status.setText(" ") self.timeLeft = qt.QLabel(self) self.l.addWidget(self.status) self.l.addWidget(self.timeLeft) self.timeLeft.setText("Estimated time left = ???? min") self.time0 = None self.html = html if htmlindex is None:htmlindex="index.html" self.htmlindex = htmlindex self.outputdir = outputdir self.table = table self.__ended = False self.__writingReport = False if actions: self.addButtons() self.show() if QTVERSION < '4.0.0': self.raiseW() else: self.raise_() def addButtons(self): self.actions = 1 self.buttonsBox = qt.QWidget(self) l = qt.QHBoxLayout(self.buttonsBox) l.addWidget(qt.HorizontalSpacer(self.buttonsBox)) self.pauseButton = qt.QPushButton(self.buttonsBox) l.addWidget(self.pauseButton) l.addWidget(qt.HorizontalSpacer(self.buttonsBox)) self.pauseButton.setText("Pause") self.abortButton = qt.QPushButton(self.buttonsBox) l.addWidget(self.abortButton) l.addWidget(qt.HorizontalSpacer(self.buttonsBox)) self.abortButton.setText("Abort") self.l.addWidget(self.buttonsBox) self.update() def customEvent(self,event): if event.dict['event'] == 'onNewFile':self.onNewFile(event.dict['file'], event.dict['filelist'], event.dict['filestep'], event.dict['filebeginoffset'], event.dict['fileendoffset']) elif event.dict['event'] == 'onImage': self.onImage (event.dict['key'], event.dict['keylist']) elif event.dict['event'] == 'onMca': self.onMca (event.dict) #event.dict['mca'], #event.dict['nmca'], #event.dict['mcastep'], #event.dict['filename'], #event.dict['key']) elif event.dict['event'] == 'onEnd': self.onEnd(event.dict) elif event.dict['event'] == 'batchPaused': self.onPause() elif event.dict['event'] == 'batchResumed':self.onResume() elif event.dict['event'] == 'reportWritten':self.onReportWritten() else: print("Unhandled event %s" % event) def onNewFile(self, file, filelist, filestep, filebeginoffset =0, fileendoffset = 0): if DEBUG: print("onNewFile: %s" % file) indexlist = list(range(0,len(filelist),filestep)) index = indexlist.index(filelist.index(file)) - filebeginoffset #print index + filebeginoffset if index == 0: self.report= None if self.html: self.htmlindex = os.path.join(self.outputdir, 'HTML') htmlindex = os.path.join(os.path.basename(file)+"_HTMLDIR", "index.html") self.htmlindex = os.path.join(self.htmlindex,htmlindex) if os.path.exists(self.htmlindex): try: os.remove(self.htmlindex) except: print("cannot delete file %s" % self.htmlindex) nfiles = len(indexlist)-filebeginoffset-fileendoffset self.status.setText("Processing file %s" % file) e = time.time() if QTVERSION < '4.0.0': self.progressBar.setTotalSteps(nfiles) self.progressBar.setProgress(index) else: self.progressBar.setMaximum(nfiles) self.progressBar.setValue(index) if self.time0 is not None: t = (e - self.time0) * (nfiles - index) self.time0 =e if t < 120: self.timeLeft.setText("Estimated time left = %d sec" % (t)) else: self.timeLeft.setText("Estimated time left = %d min" % (int(t / 60.))) else: self.time0 = e if sys.platform == 'darwin': qt.qApp.processEvents() def onImage(self,key,keylist): if DEBUG: print("onImage %s" % key) i = keylist.index(key) + 1 n = len(keylist) if QTVERSION < '4.0.0': self.imageBar.setTotalSteps(n) self.imageBar.setProgress(i) self.mcaBar.setTotalSteps(1) self.mcaBar.setProgress(0) else: self.imageBar.setMaximum(n) self.imageBar.setValue(i) self.mcaBar.setMaximum(1) self.mcaBar.setValue(0) #def onMca(self, mca, nmca, mcastep): def onMca(self, ddict): if DEBUG: print("onMca ", ddict['mca']) mca = ddict['mca'] nmca = ddict['nmca'] mcastep = ddict['mcastep'] filename = ddict['filename'] key = ddict['key'] info = ddict['info'] outputdir = ddict['outputdir'] useExistingFiles = ddict['useExistingFiles'] self.roiFit = ddict['roifit'] if self.html: try: if not self.roiFit: if mca == 0: self.__htmlReport(filename, key, outputdir, useExistingFiles, info, firstmca = True) else: self.__htmlReport(filename, key, outputdir, useExistingFiles, info, firstmca = False) except: print("ERROR on REPORT",sys.exc_info()) print(sys.exc_info()[1]) print("filename = %s key =%s " % (filename, key)) print("If your batch is stopped, please report this") print("error sending the above mentioned file and the") print("associated fit configuration file.") if QTVERSION < '4.0.0': self.mcaBar.setTotalSteps(nmca) self.mcaBar.setProgress(mca) else: self.mcaBar.setMaximum(nmca) self.mcaBar.setValue(mca) if sys.platform == 'darwin': qt.qApp.processEvents() def __htmlReport(self, filename, key, outputdir, useExistingFiles, info=None, firstmca = True): """ file=self.file fileinfo = file.GetSourceInfo() nimages = nscans = len(fileinfo['KeyList']) filename = os.path.basename(info['SourceName']) """ fitdir = os.path.join(outputdir,"HTML") if not os.path.exists(fitdir): try: os.mkdir(fitdir) except: print("I could not create directory %s" % fitdir) return fitdir = os.path.join(fitdir,filename+"_HTMLDIR") if not os.path.exists(fitdir): try: os.mkdir(fitdir) except: print("I could not create directory %s" % fitdir) return localindex = os.path.join(fitdir, "index.html") if not os.path.isdir(fitdir): print("%s does not seem to be a valid directory" % fitdir) else: outfile = filename +"_"+key+".html" outfile = os.path.join(fitdir, outfile) useExistingResult = useExistingFiles if os.path.exists(outfile): if not useExistingFiles: try: os.remove(outfile) except: print("cannot delete file %s" % outfile) useExistingResult = 0 else: useExistingResult = 0 outdir = fitdir fitdir = os.path.join(outputdir,"FIT") fitdir = os.path.join(fitdir,filename+"_FITDIR") fitfile= os.path.join(fitdir, filename +"_"+key+".fit") if not os.path.exists(fitfile): print("fit file %s does not exists!" % fitfile) return if self.report is None: #first file self.forcereport = 0 self._concentrationsFile = os.path.join(outputdir, self._rootname + "_concentrations.txt") if os.path.exists(self._concentrationsFile): """ #code removed, concentrations in McaAdvancedFitBatch.py try: os.remove(self._concentrationsFile) except: pass """ pass else: #this is to generate the concentrations file #from an already existing set of fitfiles self.forcereport = 1 if self.forcereport or (not useExistingResult): self.report = QtMcaAdvancedFitReport.QtMcaAdvancedFitReport(fitfile = fitfile, outfile = outfile, table = self.table) self.__writingReport = True a=self.report.writeReport() """ #The code below has been moved to McaAdvancedFitBatch.py if len(self.report._concentrationsTextASCII) > 1: text = "" text += "SOURCE: "+ filename +"\n" text += "KEY: "+key+"\n" text += self.report._concentrationsTextASCII + "\n" f=open(self._concentrationsFile,"a") f.write(text) f.close() """ self.__writingReport = False #qt.QApplication.postEvent(self, McaCustomEvent.McaCustomEvent({'event':'reportWritten'})) self.onReportWritten() def onEnd(self,dict): self.__ended = True if QTVERSION < '4.0.0': n = self.progressBar.progress() self.progressBar.setProgress(n+dict['filestep']) n = self.mcaBar.progress() self.mcaBar.setProgress(n+dict['mcastep']) else: n = self.progressBar.value() self.progressBar.setValue(n+dict['filestep']) n = self.mcaBar.value() self.mcaBar.setValue(n+dict['mcastep']) self.status.setText ("Batch Finished") self.timeLeft.setText("Estimated time left = 0 sec") if self.actions: self.pauseButton.hide() self.abortButton.setText("OK") if self.chunk is None: if 'savedimages' in dict: self.plotImages(dict['savedimages']) if self.html: if not self.__writingReport: directory = os.path.join(self.outputdir,"HTML") a = HtmlIndex.HtmlIndex(directory) a.buildRecursiveIndex() if dict['chunk'] is not None: if 0: #this was giving troubles using HDF5 files as input sys.exit(0) else: #this seems to work properly self.close() def onReportWritten(self): if self.__ended: directory = os.path.join(self.outputdir,"HTML") a = HtmlIndex.HtmlIndex(directory) a.buildRecursiveIndex() def onPause(self): pass def onResume(self): pass def plotImages(self,imagelist): if (sys.platform == 'win32') or (sys.platform == 'darwin'): filelist = " " for ffile in imagelist: filelist+=" %s" % ffile try: dirname = os.path.dirname(__file__) except: dirname = os.path.dirname(\ os.path.dirname(McaAdvancedFitBatch.__file__)) if (dirname[-3:] == "exe") or\ (dirname.lower().endswith(".zip")): myself = os.path.dirname(dirname) myself = os.path.join(myself, "EdfFileSimpleViewer.exe") else: myself = os.path.join(dirname, "EdfFileSimpleViewer.py") cmd = '"%s" %s ' % (myself, filelist) if 0: self.hide() qt.qApp.processEvents() os.system(cmd) self.show() else: self.__viewer = EdfFileSimpleViewer.EdfFileSimpleViewer() self.__viewer.setFileList(imagelist) self.__viewer.show() else: filelist = " " for ffile in imagelist: filelist+=" %s" % ffile try: dirname = os.path.dirname(__file__) except: dirname = os.path.dirname(\ os.path.dirname(McaAdvancedFitBatch.__file__)) if DEBUG: print("final dirname = %s" % dirname) if (dirname[-3:] == "exe") or\ (dirname.lower().endswith(".zip")): myself = os.path.dirname(dirname) myself = os.path.join(myself, "EdfFileSimpleViewer") else: myself = sys.executable+" "+os.path.join(dirname, "EdfFileSimpleViewer.py") cmd = "%s %s &" % (myself, filelist) if DEBUG: print("cmd = %s" % cmd) os.system(cmd) def main(): import getopt options = 'f' longoptions = ['cfg=','outdir=','roifit=','roi=','roiwidth=', 'overwrite=', 'filestep=', 'mcastep=', 'html=','htmlindex=', 'listfile=','cfglistfile=', 'concentrations=', 'table=', 'fitfiles=', 'filebeginoffset=','fileendoffset=','mcaoffset=', 'chunk=', 'nativefiledialogs=','selection='] filelist = None outdir = None cfg = None listfile = None cfglistfile = None selection = False roifit = 0 roiwidth = ROIWIDTH overwrite= 1 filestep = 1 html = 0 htmlindex= None mcastep = 1 table = 2 fitfiles = 1 concentrations = 0 filebeginoffset = 0 fileendoffset = 0 mcaoffset = 0 chunk = None opts, args = getopt.getopt( sys.argv[1:], options, longoptions) for opt,arg in opts: if opt in ('--cfg'): cfg = arg elif opt in ('--outdir'): outdir = arg elif opt in ('--roi','--roifit'): roifit = int(arg) elif opt in ('--roiwidth'): roiwidth = float(arg) elif opt in ('--overwrite'): overwrite= int(arg) elif opt in ('--filestep'): filestep = int(arg) elif opt in ('--mcastep'): mcastep = int(arg) elif opt in ('--html'): html = int(arg) elif opt in ('--htmlindex'): htmlindex = arg elif opt in ('--listfile'): listfile = arg elif opt in ('--cfglistfile'): cfglistfile = arg elif opt in ('--concentrations'): concentrations = int(arg) elif opt in ('--table'): table = int(arg) elif opt in ('--fitfiles'): fitfiles = int(arg) elif opt in ('--filebeginoffset'): filebeginoffset = int(arg) elif opt in ('--fileendoffset'): fileendoffset = int(arg) elif opt in ('--mcaoffset'): mcaoffset = int(arg) elif opt in ('--chunk'): chunk = int(arg) elif opt in ('--selection'): selection = int(arg) if selection: selection = True else: selection = False elif opt in ('--nativefiledialogs'): if int(arg): PyMcaDirs.nativeFileDialogs = True else: PyMcaDirs.nativeFileDialogs = False if listfile is None: filelist=[] for item in args: filelist.append(item) selection = None else: if selection: tmpDict = ConfigDict.ConfigDict() tmpDict.read(listfile) tmpDict = tmpDict['PyMcaBatch'] filelist = tmpDict['filelist'] if type(filelist) == type(""): filelist = [filelist] selection = tmpDict['selection'] else: fd = open(listfile, 'rb') filelist = fd.readlines() fd.close() for i in range(len(filelist)): filelist[i]=filelist[i].decode(sys.getfilesystemencoding()).replace('\n','') selection = None if cfglistfile is not None: fd = open(cfglistfile, 'rb') cfg = fd.readlines() fd.close() for i in range(len(cfg)): cfg[i]=cfg[i].decode(sys.getfilesystemencoding()).replace('\n','') app=qt.QApplication(sys.argv) winpalette = qt.QPalette(qt.QColor(230,240,249),qt.QColor(238,234,238)) app.setPalette(winpalette) if len(filelist) == 0: qt.QObject.connect(app,qt.SIGNAL("lastWindowClosed()"),app, qt.SLOT("quit()")) w = McaBatchGUI(actions=1) if QTVERSION < '4.0.0': app.setMainWidget(w) w.show() app.exec_loop() else: w.show() w.raise_() app.exec_() else: qt.QObject.connect(app,qt.SIGNAL("lastWindowClosed()"),app, qt.SLOT("quit()")) text = "Batch from %s to %s" % (os.path.basename(filelist[0]), os.path.basename(filelist[-1])) window = McaBatchWindow(name=text,actions=1, outputdir=outdir,html=html, htmlindex=htmlindex, table=table, chunk = chunk) if html:fitfiles=1 try: b = McaBatch(window,cfg,filelist,outdir,roifit=roifit,roiwidth=roiwidth, overwrite = overwrite, filestep=filestep, mcastep=mcastep, concentrations=concentrations, fitfiles=fitfiles, filebeginoffset=filebeginoffset,fileendoffset=fileendoffset, mcaoffset=mcaoffset, chunk=chunk, selection=selection) except: msg = qt.QMessageBox() msg.setIcon(qt.QMessageBox.Critical) msg.setText("%s" % sys.exc_info()[1]) if QTVERSION < '4.0.0': msg.exec_loop() else: msg.exec_() return def cleanup(): b.pleasePause = 0 b.pleaseBreak = 1 b.wait() qt.qApp.processEvents() def pause(): if b.pleasePause: b.pleasePause=0 window.pauseButton.setText("Pause") else: b.pleasePause=1 window.pauseButton.setText("Continue") qt.QObject.connect(window.pauseButton,qt.SIGNAL("clicked()"),pause) qt.QObject.connect(window.abortButton,qt.SIGNAL("clicked()"),window.close) qt.QObject.connect(app,qt.SIGNAL("aboutToQuit()"),cleanup) window._rootname = "%s"% b._rootname window.show() b.start() if QTVERSION < '4.0.0': app.setMainWidget(window) app.exec_loop() else: app.exec_() if __name__ == "__main__": main() # PyMcaBatch.py --cfg=/mntdirect/_bliss/users/sole/COTTE/WithLead.cfg --outdir=/tmp/ /mntdirect/_bliss/users/sole/COTTE/ch09/ch09__mca_0003_0000_0007.edf /mntdirect/_bliss/users/sole/COTTE/ch09/ch09__mca_0003_0000_0008.edf /mntdirect/_bliss/users/sole/COTTE/ch09/ch09__mca_0003_0000_0009.edf /mntdirect/_bliss/users/sole/COTTE/ch09/ch09__mca_0003_0000_0010.edf /mntdirect/_bliss/users/sole/COTTE/ch09/ch09__mca_0003_0000_0011.edf /mntdirect/_bliss/users/sole/COTTE/ch09/ch09__mca_0003_0000_0012.edf /mntdirect/_bliss/users/sole/COTTE/ch09/ch09__mca_0003_0000_0013.edf & # PyMcaBatch.exe --cfg=E:/COTTE/WithLead.cfg --outdir=C:/tmp/ E:/COTTE/ch09/ch09__mca_0003_0000_0007.edf E:/COTTE/ch09/ch09__mca_0003_0000_0008.edf