#!/usr/bin/env python
# -*- coding: utf-8 -*-
#GSAS-II autointegration routines
########### SVN repository information ###################
# $Date: 2023-05-11 18:08:12 -0500 (Thu, 11 May 2023) $
# $Author: toby $
# $Revision: 5577 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIIntPDFtool.py $
# $Id: GSASIIIntPDFtool.py 5577 2023-05-11 23:08:12Z toby $
########### SVN repository information ###################
'''
'''
# Autointegration GSASIIimgGUI and GSASIIimage, hacked for stand-alone use
#
# idea: select image file type & set filter from that
#
from __future__ import division, print_function
import os
import copy
import glob
import time
import re
import math
import sys
import wx
import wx.lib.mixins.listctrl as listmix
import wx.grid as wg
import numpy as np
import GSASIIpath
GSASIIpath.SetBinaryPath(True)
GSASIIpath.SetVersionNumber("$Revision: 5577 $")
import GSASIIIO as G2IO
import GSASIIctrlGUI as G2G
import GSASIIobj as G2obj
import GSASIIimgGUI as G2imG
import GSASIIfiles as G2fil
import GSASIIscriptable as G2sc
import multiprocessing as mp
try: # fails during doc build
wxMainFrameStyle = wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX
except:
wxMainFrameStyle = None
[docs]
class AutoIntFrame(wx.Frame):
'''Creates a wx.Frame window for the Image AutoIntegration.
The intent is that this will be used as a non-modal dialog window.
Implements a Start button that morphs into a pause and resume button.
This button starts a processing loop that is repeated every
:meth:`PollTime` seconds.
:param wx.Frame G2frame: main GSAS-II frame
:param float PollTime: frequency in seconds to repeat calling the
processing loop. (Default is 30.0 seconds.)
'''
def __init__(self,G2frame,PollTime=30.0):
def OnStart(event):
'''Called when the start button is pressed. Changes button label
to Pause. When Pause is pressed the label changes to Resume.
When either Start or Resume is pressed, the processing loop
is started. When Pause is pressed, the loop is stopped.
'''
self.Pause = False
# change button label
if self.btnstart.GetLabel() != 'Pause':
self.btnstart.SetLabel('Pause')
self.Status.SetStatusText('Press Pause to delay integration or Reset to prepare to reintegrate all images')
if self.timer.IsRunning(): self.timer.Stop()
self.PreventTimerReEntry = False
if self.StartLoop():
G2G.G2MessageBox(self,'Error in setting up integration. See console')
return
# delete pool of slaved interpreters in case input has changed
if self.MPpool:
self.MPpool.terminate()
self.MPpool = None
# if self.ncores >= 1: # debug
if self.ncores > 1:
# print('Creating pool of ',self.ncores,'cores') # debug
self.MPpool = mp.Pool(self.ncores)
self.OnTimerLoop(None) # run once immediately
if not self.Pause:
# no pause, so start timer to check for new files
self.timer.Start(int(1000*PollTime),oneShot=False)
return
# we will get to this point if Paused
self.OnPause()
def OnReset(event):
'''Called when Reset button is pressed. This stops the
processing loop and resets the list of integrated files so
all images can be reintegrated.
'''
self.btnstart.SetLabel('Restart')
self.Status.SetStatusText('Press Restart to reload and re-integrate images matching filter')
if self.timer.IsRunning(): self.timer.Stop()
self.Reset = True
self.Pause = True
self.ProcessedList = []
self.ShowMatchingFiles(None)
def OnQuit(event):
'''Stop the processing loop and close the Frame
'''
if self.timer.IsRunning(): self.timer.Stop() # make sure we stop first
wx.CallAfter(self.Destroy)
def OnBrowse(event):
'''Responds when the Browse button is pressed to load a file.
The routine determines which button was pressed and gets the
appropriate file type and loads it into the appropriate place
in the dict.
'''
if btn3 == event.GetEventObject():
dlg = wx.DirDialog(
self, 'Select directory for output files',
self.params['outdir'],wx.DD_DEFAULT_STYLE)
dlg.CenterOnParent()
try:
if dlg.ShowModal() == wx.ID_OK:
self.params['outdir'] = dlg.GetPath()
fInp3.SetValue(self.params['outdir'])
finally:
dlg.Destroy()
return
def showPDFctrls(event):
'''Called to show or hide AutoPDF widgets. Note that TextCtrl's
must be included in the sizer layout with .Show(True) before
.Show(False) will work properly.
'''
TestInput()
if len(self.pdfList) == 0 or self.params['TableMode']:
lbl4b.SetValue(False)
self.params['ComputePDF'] = False
lbl4b.Enable(False)
else:
lbl4b.Enable(True)
for w in [self.pbkg[i][4] for i in (0,1,2)]:
w.Enable(self.params['ComputePDF'])
w.Show(self.params['ComputePDF'])
#for o in pdfwidgets+[self.pbkg[i][2] for i in (0,1,2)]:
for o in pdfwidgets+[self.pdfSel]+[self.pbkg[i][1] for i in range(3)]:
o.Enable(self.params['ComputePDF'])
if self.params['ComputePDF']:
c = "black"
else:
c = "gray"
for l in ([lbl4,lbl4a,lbl5,lbl5a,lbl5b]
+[self.pbkg[i][0] for i in (0,1,2)]
+[self.pbkg[i][5] for i in (0,1,2)]):
l.SetForegroundColour(c)
l.SetBackgroundColour("white")
checkPDFselection()
self.SendSizeEvent()
def GetGPXInputFile(event):
'Get and read input from input GPX file'
pth = self.params['readdir']
lbl = 'Select a project input file'
filtyp = 'project file (.gpx)|*.gpx'
if event is not None:
dlg = wx.FileDialog(self,lbl, pth,
style=wx.FD_OPEN,wildcard=filtyp)
dlg.CenterOnParent()
if dlg.ShowModal() == wx.ID_OK:
self.gpxin[3] = dlg.GetPath()
dlg.Destroy()
if not os.path.exists(self.gpxin[3]):
G2G.G2MessageBox(self,'Error: file {} not found.'.format(self.gpxin[3]))
return
SetGPXInputFile()
def SetGPXInputFile():
gpx = G2sc.G2Project(self.gpxin[3])
self.imgList = gpx.images()
self.histList = gpx.histograms()
self.pdfList = gpx.pdfs()
if not self.imgList:
G2G.G2MessageBox(self,'Error: no images in {}.'.format(self.gpxin[3]))
return
self.gpxin[1].SetValue(self.gpxin[3])
self.imprm[1].Clear()
self.imprm[1].AppendItems([i.name for i in self.imgList])
if len(self.imgList) == 1:
self.imprm[1].SetSelection(0)
self.maskfl[1].Clear()
self.maskfl[1].AppendItems(['']+[i.name for i in self.imgList])
for i in range(3):
self.pbkg[i][1].Clear()
self.pbkg[i][1].AppendItems(['']+[i.name for i in self.histList])
self.pdfSel.Clear()
self.pdfSel.AppendItems([i.name for i in self.pdfList])
showPDFctrls(None)
def TestInput(*args,**kwargs):
'''Determine if the start button should be enabled and
ask for the exporter type with ambiguous extensions
'''
for dfmt,obj in self.fmtlist.items():
fmt = dfmt[1:]
if not self.params['outsel'][fmt]: continue
if fmt in self.multipleFmtChoices: continue
if type(obj) is not list: continue # only one exporter for this
choices = []
for e in obj:
choices.append(e.formatName)
if len(choices) == 0:
print('Error: why 0 choices in TestInput?')
continue
if len(choices) == 1:
print('Error: why 1 choice in TestInput?')
self.multipleFmtChoices[fmt] = obj[0].formatName
continue
# select the format here
dlg = G2G.G2SingleChoiceDialog(self,
'There is more than one format with a '+
'.{} output. Choose the one to use'.format(fmt),
'Choose output format',choices)
dlg.CenterOnParent()
dlg.clb.SetSelection(0) # force a selection
if dlg.ShowModal() == wx.ID_OK and dlg.GetSelection() >= 0:
self.multipleFmtChoices[fmt] = choices[dlg.GetSelection()]
dlg.Destroy()
writingSomething = False
writingPDF = False
# is at least one output file selected?
for dfmt in self.fmtlist:
fmt = dfmt[1:]
if self.params['outsel'][fmt]:
writingSomething = True
break
if self.params['ComputePDF']:
for fmt in self.PDFformats:
if self.params['outsel'][fmt]:
writingPDF = writingSomething = True
break
if not writingSomething:
self.EnableIntButtons(False)
return
# do we have integration input?
if not self.params['TableMode']:
if not self.gpxin[3]:
self.EnableIntButtons(False)
return
elif not os.path.exists(self.gpxin[3]):
self.EnableIntButtons(False)
return
elif len(self.imgList) == 0:
self.EnableIntButtons(False)
return
else:
self.EnableIntButtons(True)
else:
if self.ImgTblParms:
self.EnableIntButtons(True)
else:
self.EnableIntButtons(False)
return
# do we have PDF input, if requested
if self.params['ComputePDF']:
if len(self.pdfList) == 0 or not writingPDF:
self.EnableIntButtons(False)
elif 'Error' in self.formula:
self.EnableIntButtons(False)
def checkPDFselection():
'Read PDF entry from input GPX file & show in GUI'
pdfEntry = self.pdfSel.GetStringSelection()
if not self.pdfList:
self.params['ComputePDF'] = False
lbl4b.Enable(False)
return
else:
lbl4b.Enable(True)
if pdfEntry not in [i.name for i in self.pdfList]:
# strange something -- not selected
self.pdfSel.SetSelection(0)
pdfEntry = self.pdfSel.GetStringSelection()
if self.gpxInp is None or self.gpxInp.filename != self.gpxin[3]:
self.gpxInp = G2sc.G2Project(self.gpxin[3])
try:
PDFobj = self.gpxInp.pdf(pdfEntry)
except KeyError:
print("PDF entry not found: {}".format(pdfEntry))
return
histNames = [i.name for i in self.histList]
for i,lbl in enumerate(('Sample Bkg.','Container',
'Container Bkg.')):
self.pbkg[i][4].SetValue(str(PDFobj.data['PDF Controls'][lbl]['Mult']))
self.pbkg[i][6] = PDFobj.data['PDF Controls'][lbl]['Mult']
try:
i = 1 + histNames.index(PDFobj.data['PDF Controls'][lbl]['Name'])
self.pbkg[i][1].SetSelection(i)
except ValueError:
i = 0
self.pbkg[i][1].SetSelection(0)
if PDFobj.data['PDF Controls'][lbl]['Name']:
print('PDF {} hist entry {} not found'.format(
lbl,PDFobj.data['PDF Controls'][lbl]['Name']))
PDFobj.data['PDF Controls'][lbl]['Name'] = ''
self.formula = ''
for el in PDFobj.data['PDF Controls']['ElList']:
i = PDFobj.data['PDF Controls']['ElList'][el]['FormulaNo']
if i <= 0:
continue
elif i == 1:
if self.formula: self.formula += ' '
self.formula += '{}'.format(el)
else:
if self.formula: self.formula += ' '
self.formula += '{}({:.1f})'.format(el,i)
if not self.formula:
self.formula = 'Error: no chemical formula'
lbl5b.SetLabel(self.formula)
TestInput()
def ShowbyMode():
'create table or non-table integration section of GUI'
intPrmSizer.Clear(True)
if not self.params['TableMode']:
sizer = wx.BoxSizer(wx.HORIZONTAL)
self.gpxin[0] = wx.StaticText(mnpnl, wx.ID_ANY,'Project (gpx) file:')
sizer.Add(self.gpxin[0])
self.gpxin[1] = G2G.ValidatedTxtCtrl(mnpnl,self.gpxin,3,
OKcontrol=TestInput,OnLeave=TestInput)
sizer.Add(self.gpxin[1],1,wx.EXPAND,1)
self.gpxin[2] = wx.Button(mnpnl, wx.ID_ANY, "Browse")
self.gpxin[2].Bind(wx.EVT_BUTTON, GetGPXInputFile)
sizer.Add(self.gpxin[2],0,wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
intPrmSizer.Add(sizer,0,wx.EXPAND,0)
sizer = wx.BoxSizer(wx.HORIZONTAL)
self.imprm[0] = wx.StaticText(mnpnl, wx.ID_ANY,'Image parms from:')
sizer.Add(self.imprm[0])
self.imprm[3] = 0
self.imprm[1] = G2G.G2ChoiceButton(mnpnl,[''],self.imprm,3,onChoice=TestInput)
sizer.Add(self.imprm[1],1,wx.EXPAND,1)
intPrmSizer.Add(sizer,0,wx.EXPAND,0)
sizer = wx.BoxSizer(wx.HORIZONTAL)
self.maskfl[0] = wx.StaticText(mnpnl, wx.ID_ANY,'Mask parms from:')
sizer.Add(self.maskfl[0])
self.maskfl[3] = 0
self.maskfl[1] = G2G.G2ChoiceButton(mnpnl,[''],self.maskfl,3,onChoice=TestInput)
sizer.Add(self.maskfl[1],1,wx.EXPAND,1)
intPrmSizer.Add(sizer,0,wx.EXPAND,0)
else:
sizer = wx.BoxSizer(wx.HORIZONTAL)
self.table = [None,None,None,None]
self.table[0] = wx.Button(mnpnl, wx.ID_ANY, "Create table")
sizer.Add(self.table[0],0,wx.ALIGN_LEFT|wx.ALL,5)
self.table[0].Bind(wx.EVT_BUTTON, OnTableButton)
self.table[1] = wx.Button(mnpnl, wx.ID_ANY, "Read table")
sizer.Add(self.table[1],0,wx.ALIGN_LEFT|wx.ALL,5)
self.table[1].Bind(wx.EVT_BUTTON, OnTableButton)
self.table[2] = wx.Button(mnpnl, wx.ID_ANY, "Edit table")
sizer.Add(self.table[2],0,wx.ALIGN_LEFT|wx.ALL,5)
self.table[2].Bind(wx.EVT_BUTTON, OnTableButton)
#self.table[3] = wx.Button(mnpnl, wx.ID_ANY, "Save table")
#sizer.Add(self.table[3],0,wx.ALIGN_LEFT|wx.ALL,5)
#self.table[3].Bind(wx.EVT_BUTTON, OnTableButton)
intPrmSizer.Add(sizer,0,wx.EXPAND,0)
# enable/disable based on status of files/table
TestInput()
mnsizer.Fit(self)
def OnTableButton(event):
'''Called to edit/create the distance-dependent parameter look-up table.
'''
pth = self.params['readdir']
readFileList = []
parms,fileList = [], []
if event.GetEventObject() == self.table[0]:
dlg = wx.FileDialog(self, 'Build new table by selecting image control files', pth,
style=wx.FD_OPEN| wx.FD_MULTIPLE,
wildcard='Image control files (.imctrl)|*.imctrl')
dlg.CenterOnParent()
if dlg.ShowModal() == wx.ID_OK:
readFileList = dlg.GetPaths()
dlg.Destroy()
if len(readFileList) <= 0: return
elif event.GetEventObject() == self.table[1]:
dlg = wx.FileDialog(self, 'Reload table by selecting saved file', pth,
style=wx.FD_OPEN,
wildcard='Integration table (*.imtbl)|*.imtbl')
dlg.CenterOnParent()
if dlg.ShowModal() == wx.ID_OK:
readFileList = [dlg.GetPath()]
dlg.Destroy()
if len(readFileList) <= 0: return
elif event.GetEventObject() == self.table[2]:
parms = copy.deepcopy(self.ImgTblParms)
fileList = copy.copy(self.IMfileList)
if not parms:
G2G.G2MessageBox(self,'Create or Read table first')
return
dlg = None
try:
dlg = G2imG.IntegParmTable(self,parms,fileList,readFileList)
dlg.CenterOnParent()
if dlg.ShowModal() == wx.ID_OK:
self.params['InterVals'] = SetupInterpolation(dlg)
self.ImgTblParms = dlg.ReadImageParmTable()
self.IMfileList = dlg.IMfileList
self.params['TableMode'] = True
self.params['ControlsTable'] = {}
self.params['MaskTable'] = {}
for f,m in zip(self.IMfileList,self.ImgTblParms[-1]):
n = os.path.split(f)[1]
if n in self.params['ControlsTable']:
print('Warning overwriting entry {}'.format(n))
self.params['ControlsTable'][n] = G2imG.ReadControls(f)
if m and os.path.exists(m):
self.params['MaskTable'][n] = G2imG.ReadMask(m)
elif m != "(none)":
print("Error: Mask file {} not found".format(m))
else:
self.params['TableMode'] = False
self.params['ControlsTable'] = {}
self.params['MaskTable'] = {}
self.imageBase = G2frame.Image
finally:
if dlg: dlg.Destroy()
TestInput()
##################################################
# beginning of __init__ processing
##################################################
self.G2frame = G2frame
self.ImgTblParms = None
self.IMfileList = None
self.params = {}
self.Reset = False
self.Pause = False
self.PreventReEntryShowMatch = False
self.PreventTimerReEntry = False
self.params['ControlsTable'] = {}
self.params['MaskTable'] = {}
G2sc.LoadG2fil()
self.fmtlist = G2sc.exportersByExtension.get('powder',{})
self.fmtlist['.gpx'] = None
self.timer = wx.Timer()
self.timer.Bind(wx.EVT_TIMER,self.OnTimerLoop)
self.imageBase = G2frame.Image
self.params['ComputePDF'] = False
self.params['pdfDmax'] = 0.0
self.params['pdfprm'] = ''
self.params['optPDF'] = True
self.params['TableMode'] = False
self.params['outsel'] = {}
self.formula = 'Error'
self.pdfControls = {}
self.imgList = []
self.histList = []
self.pdfList = []
self.Scale = [1.0,]
self.ProcessedList = [] # files that have been integrated
self.currImageList = [] # files that will be integrated
self.gpxInp = None
self.gpxin = [None,None,None,'']
self.imprm = [None,None,None,'']
self.maskfl = [None,None,None,'']
self.ncores = mp.cpu_count()//2
self.MPpool = None
self.params['readdir'] = os.getcwd()
self.params['filter'] = '*.tif'
self.params['outdir'] = os.getcwd()
self.PDFformats = ('I(Q)', 'S(Q)', 'F(Q)', 'G(r)', 'PDFgui')
self.multipleFmtChoices = {}
#GSASIIpath.IPyBreak_base()
wx.Frame.__init__(self, None, title='Automatic Integration',
style=wxMainFrameStyle)
self.Status = self.CreateStatusBar()
self.Status.SetStatusText('Press Start to load and integrate images matching filter')
mnpnl = wx.Panel(self)
mnsizer = wx.BoxSizer(wx.VERTICAL)
# box for integration controls & masks input
intSizer = wx.BoxSizer(wx.VERTICAL)
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add((-1,-1),1,wx.EXPAND,1)
sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Calibration/Integration parameters'))
sizer.Add((-1,-1),1,wx.EXPAND,1)
intSizer.Add(sizer,1,wx.EXPAND,1)
def ontblModeBtn(event):
if tblModeBtn.GetValue():
self.params['TableMode'] = True
else:
self.params['TableMode'] = False
ShowbyMode()
tblModeBtn = wx.CheckBox(mnpnl,label='Use distance lookup table')
tblModeBtn.SetValue(False)
tblModeBtn.Bind(wx.EVT_CHECKBOX, ontblModeBtn)
intSizer.Add(tblModeBtn)
mnsizer.Add(intSizer,0,wx.EXPAND,0)
intPrmSizer = wx.BoxSizer(wx.VERTICAL)
mnsizer.Add(intPrmSizer,0,wx.EXPAND,0)
# file filter stuff
mnsizer.Add((-1,15))
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Read images from '))
self.readDir = G2G.ValidatedTxtCtrl(mnpnl,self.params,'readdir',
OnLeave=self.ShowMatchingFiles,size=(200,-1))
sizer.Add(self.readDir,1,wx.EXPAND,1)
btn3 = wx.Button(mnpnl, wx.ID_ANY, "Browse")
btn3.Bind(wx.EVT_BUTTON, self.SetSourceDir)
sizer.Add(btn3,0,wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
mnsizer.Add(sizer,0,wx.EXPAND,0)
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add((-1,-1),1,wx.EXPAND,1)
sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,' Image filter'))
flterInp = G2G.ValidatedTxtCtrl(mnpnl,self.params,'filter',
OnLeave=self.ShowMatchingFiles)
sizer.Add(flterInp)
mnsizer.Add(sizer,0,wx.EXPAND,0)
self.ListBox = wx.ListBox(mnpnl,size=(-1,100))
mnsizer.Add(self.ListBox,1,wx.EXPAND,1)
self.ShowMatchingFiles(None)
# box for output selections
mnsizer.Add((-1,15))
lbl = wx.StaticBox(mnpnl, wx.ID_ANY, "Integration output")
lblsizr = wx.StaticBoxSizer(lbl, wx.VERTICAL)
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Write to: '),0,wx.ALIGN_CENTER_VERTICAL)
fInp3 = G2G.ValidatedTxtCtrl(mnpnl,self.params,'outdir',notBlank=False,size=(300,-1))
sizer.Add(fInp3,1,wx.EXPAND)
btn3 = wx.Button(mnpnl, wx.ID_ANY, "Browse")
btn3.Bind(wx.EVT_BUTTON, OnBrowse)
sizer.Add(btn3,0,wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
lblsizr.Add(sizer,0,wx.EXPAND)
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Select format(s):'))
for dfmt in sorted(self.fmtlist):
sizer.Add((6,2)) # add a bit of extra space
fmt = dfmt[1:]
if fmt not in self.params['outsel']: self.params['outsel'][fmt] = False
btn = G2G.G2CheckBox(mnpnl,dfmt,self.params['outsel'],fmt,
OnChange=TestInput)
sizer.Add(btn)
lblsizr.Add(sizer)
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Separate dir for each format: '))
self.params['SeparateDir'] = False
sizer.Add(G2G.G2CheckBox(mnpnl,'',self.params,'SeparateDir'))
lblsizr.Add(sizer)
mnsizer.Add(lblsizr,0,wx.EXPAND,1)
mnsizer.Add((-1,15))
lbl = wx.StaticBox(mnpnl, wx.ID_ANY, "PDF settings")
pdfwidgets = []
lblsizr = wx.StaticBoxSizer(lbl, wx.VERTICAL)
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Autocompute PDF:'),0,wx.ALIGN_CENTER_VERTICAL)
lbl4b = G2G.G2CheckBox(mnpnl,'',self.params,'ComputePDF',
OnChange=showPDFctrls)
sizer.Add(lbl4b)
lbl4a = wx.StaticText(mnpnl, wx.ID_ANY,'Max detector distance: ')
sizer.Add(lbl4a,0,wx.ALIGN_CENTER_VERTICAL)
fInp4a = G2G.ValidatedTxtCtrl(mnpnl,self.params,'pdfDmax',xmin=0.0)
pdfwidgets.append(fInp4a)
sizer.Add(fInp4a,0,wx.ALIGN_CENTER_VERTICAL)
cOpt = G2G.G2CheckBox(mnpnl,'Optimize',self.params,'optPDF')
pdfwidgets.append(cOpt)
sizer.Add(cOpt)
lblsizr.Add(sizer,0)
sizer = wx.BoxSizer(wx.HORIZONTAL)
lbl4 = wx.StaticText(mnpnl, wx.ID_ANY,'PDF control: ')
sizer.Add(lbl4,0,wx.ALIGN_CENTER_VERTICAL)
self.pdfSel = G2G.G2ChoiceButton(mnpnl,[''],self.params,'pdfprm',
onChoice=checkPDFselection)
sizer.Add(self.pdfSel,1,wx.EXPAND,1)
lblsizr.Add(sizer,0,wx.EXPAND)
sizer = wx.BoxSizer(wx.HORIZONTAL)
lbl5a = wx.StaticText(mnpnl, wx.ID_ANY,'Chemical formula: ')
sizer.Add(lbl5a)
lbl5b = wx.StaticText(mnpnl, wx.ID_ANY,'(formula)')
sizer.Add(lbl5b)
lblsizr.Add(sizer,0,wx.EXPAND)
sizer = wx.BoxSizer(wx.HORIZONTAL)
lbl5 = wx.StaticText(mnpnl, wx.ID_ANY,'Select format(s):')
sizer.Add(lbl5)
for fmt in self.PDFformats:
sizer.Add((6,2)) # add a bit of extra space
if fmt not in self.params['outsel']: self.params['outsel'][fmt] = False
btn = G2G.G2CheckBox(mnpnl,fmt,self.params['outsel'],fmt,
OnChange=TestInput)
sizer.Add(btn)
pdfwidgets.append(btn)
lblsizr.Add(sizer,0,wx.EXPAND)
self.pbkg = 3*[None]
for i,lbl in enumerate((' Sample bkg:',' Container:',
'Container bkg:')):
self.pbkg[i] = [None,None,None,'',None,None,-1.0]
sizer = wx.BoxSizer(wx.HORIZONTAL)
self.pbkg[i][0] = wx.StaticText(mnpnl, wx.ID_ANY,lbl)
sizer.Add(self.pbkg[i][0])
self.pbkg[i][1] = G2G.G2ChoiceButton(mnpnl,[''],self.pbkg[i],3)
sizer.Add(self.pbkg[i][1],1,wx.EXPAND,1)
self.pbkg[i][5] = wx.StaticText(mnpnl, wx.ID_ANY,' mult:')
sizer.Add(self.pbkg[i][5])
self.pbkg[i][4] = G2G.ValidatedTxtCtrl(mnpnl,self.pbkg[i],6,
(6,3),typeHint=float,size=(50,-1),
OnLeave=TestInput,notBlank=False)
sizer.Add(self.pbkg[i][4])
lblsizr.Add(sizer,0,wx.EXPAND,0)
mnsizer.Add(lblsizr,0,wx.EXPAND,1)
# buttons on bottom
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add((20,-1))
self.btnstart = wx.Button(mnpnl, wx.ID_ANY, "Start")
self.btnstart.Bind(wx.EVT_BUTTON, OnStart)
sizer.Add(self.btnstart)
self.btnreset = wx.Button(mnpnl, wx.ID_ANY, "Reset")
self.btnreset.Bind(wx.EVT_BUTTON, OnReset)
sizer.Add(self.btnreset)
sizer.Add((20,-1),wx.EXPAND,1)
sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,' cores:'))
spin = wx.SpinCtrl(mnpnl, wx.ID_ANY,size=(50,-1))
spin.SetRange(1, mp.cpu_count())
# spin.SetRange(0, mp.cpu_count()) # debug
spin.SetValue(self.ncores)
def _onSpin(event):
if event: event.Skip()
self.ncores = spin.GetValue()
spin.Bind(wx.EVT_SPINCTRL, _onSpin)
spin.Bind(wx.EVT_KILL_FOCUS, _onSpin)
sizer.Add(spin)
sizer.Add((20,-1),wx.EXPAND,1)
self.btnclose = wx.Button(mnpnl, wx.ID_ANY, "Exit")
self.btnclose.Bind(wx.EVT_BUTTON, OnQuit)
self.EnableIntButtons(False)
sizer.Add(self.btnclose)
sizer.Add((20,-1))
mnsizer.Add(sizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP,5)
# finish up window
mnpnl.SetSizer(mnsizer)
#OnRadioSelect(None) # disable widgets
mnsizer.Fit(self)
ShowbyMode()
if len(sys.argv) > 1:
fil = os.path.splitext(sys.argv[1])[0]+'.gpx'
if os.path.exists(fil):
self.gpxin[3] = fil
SetGPXInputFile()
showPDFctrls(None)
[docs]
def SetSourceDir(self,event):
'''Use a dialog to get a directory for image files
'''
dlg = wx.DirDialog(self, 'Select directory for image files',
self.params['readdir'],wx.DD_DEFAULT_STYLE)
dlg.CenterOnParent()
try:
if dlg.ShowModal() == wx.ID_OK:
self.params['readdir'] = dlg.GetPath()
self.readDir.SetValue(self.params['readdir'])
self.ShowMatchingFiles(None)
finally:
dlg.Destroy()
return
[docs]
def ShowMatchingFiles(self,value,invalid=False,**kwargs):
'''Find and image files matching the image
file directory (self.params['readdir']) and the image file filter
(self.params['filter']) and add this information to the GUI list box
'''
if invalid: return
if self.PreventReEntryShowMatch: return
self.PreventReEntryShowMatch = True
filmsg = ""
self.currImageList = []
if os.path.exists(self.params['readdir']):
imageList = sorted(
glob.glob(os.path.join(self.params['readdir'],self.params['filter'])))
if not imageList:
msg = 'Warning: No files match search string '+os.path.join(
self.params['readdir'],self.params['filter'])
else:
for fil in imageList:
if fil not in self.ProcessedList:
filmsg += '\n '+fil
self.currImageList.append(fil)
if filmsg:
msg = 'Files to integrate from '+os.path.join(
self.params['readdir'],self.params['filter'])+filmsg
else:
msg = 'No files found to process in '+self.params['readdir']
else:
msg = 'Warning, does not exist: '+self.params['readdir']
if self.ProcessedList:
msg += '\nIntegrated files:'
for fil in self.ProcessedList:
msg += '\n '+fil
self.ListBox.Clear()
self.ListBox.AppendItems(msg.split('\n'))
self.PreventReEntryShowMatch = False
return
[docs]
def OnPause(self):
'''Respond to Pause, changes text on button/Status line, if needed
Stops timer
self.Pause should already be True
'''
if self.timer.IsRunning(): self.timer.Stop()
if self.btnstart.GetLabel() == 'Restart':
return
if self.btnstart.GetLabel() != 'Resume':
print('\nPausing autointegration\n')
self.btnstart.SetLabel('Resume')
self.Status.SetStatusText(
'Press Resume to continue integration or Reset to prepare to reintegrate all images')
self.Pause = True
def EnableIntButtons(self,flag):
for item in (self.btnstart,self.btnreset): item.Enable(flag)
[docs]
def StartLoop(self):
'''Prepare to start autointegration timer loop.
Save current Image params for use in future integrations
also label the window so users understand what is being used
'''
print('\nStarting new autointegration\n')
# make sure all output directories exist
if self.params['SeparateDir']:
for dfmt in self.fmtlist:
if not self.params['outsel'][dfmt[1:]]: continue
dir = os.path.join(self.params['outdir'],dfmt[1:])
if not os.path.exists(dir): os.makedirs(dir)
else:
if not os.path.exists(self.params['outdir']):
os.makedirs(self.params['outdir'])
if self.Reset: # special things to do after Reset has been pressed
self.G2frame.IntegratedList = []
wx.Yield()
self.Reset = False
if self.params['ComputePDF'] and self.params['SeparateDir']:
for fmt in self.PDFformats:
if not self.params['outsel'][fmt]: continue
dir = os.path.join(self.params['outdir'],
fmt.replace("(","_").replace(")",""))
if not os.path.exists(dir): os.makedirs(dir)
return False
[docs]
def ArgGen(self,PDFobj,imgprms,mskprms,xydata):
'''generator for arguments for integration/PDF calc
'''
for newImage in self.currImageList:
self.Pause |= self.G2frame.PauseIntegration
if self.Pause:
self.OnPause()
self.PreventTimerReEntry = False
self.Raise()
return
TableMode = self.params['TableMode']
ComputePDF = self.params['ComputePDF']
SeparateDir = self.params['SeparateDir']
optPDF = self.params['optPDF']
outdir = self.params['outdir']
calcModes = (TableMode,ComputePDF,SeparateDir,optPDF)
InterpVals = self.params.get('InterVals')
outputSelect = self.params['outsel']
PDFformats = self.PDFformats
outputModes = (outputSelect,PDFformats,self.fmtlist,outdir,
self.multipleFmtChoices)
if PDFobj:
PDFdict = PDFobj.data
else:
PDFdict = None
yield (newImage,imgprms,mskprms,xydata,PDFdict,InterpVals,calcModes,outputModes)
[docs]
def OnTimerLoop(self,event):
'''A method that is called every :meth:`PollTime` seconds that is
used to check for new files and process them. Integrates new images.
Also optionally sets up and computes PDF.
This is called only after the "Start" button is pressed (then its label reads "Pause").
'''
if GSASIIpath.GetConfigValue('debug'):
import datetime
print ("DBG_Timer tick at {:%d %b %Y %H:%M:%S}\n".format(datetime.datetime.now()))
if self.PreventTimerReEntry: return
self.PreventTimerReEntry = True
self.ShowMatchingFiles(None)
if not self.currImageList:
self.PreventTimerReEntry = False
return
updateList = False
# get input for integration
imgprms = mskprms = None
if not self.params['TableMode']:
# read in image controls/masks, used below in loop. In Table mode
# we will get this image-by image.
gpxinp = G2sc.G2Project(self.gpxin[3])
print('reading template project',gpxinp.filename)
img = gpxinp.image(self.imprm[1].GetStringSelection())
imgprms = img.getControls(True)
if self.maskfl[1].GetStringSelection().strip():
img = gpxinp.image(self.maskfl[1].GetStringSelection())
mskprms = img.getMasks()
# setup shared input for PDF computation (for now will not be table mode)
xydata = {}
if self.params['ComputePDF']:
pdfEntry = self.pdfSel.GetStringSelection()
try:
PDFobj = gpxinp.pdf(pdfEntry)
except KeyError:
print("PDF entry not found: {}".format(pdfEntry))
# update with GUI input
for i,lbl in enumerate(('Sample Bkg.','Container',
'Container Bkg.')):
name = self.pbkg[i][1].GetStringSelection()
try:
xydata[lbl] = gpxinp.histogram(name).data['data']
except AttributeError:
pass
PDFobj.data['PDF Controls'][lbl]['Mult'] = self.pbkg[i][6]
PDFobj.data['PDF Controls'][lbl]['Name'] = name
else:
PDFobj = None
if self.MPpool:
self.MPpool.imap_unordered(ProcessImageMP,
self.ArgGen(PDFobj,imgprms,mskprms,xydata))
else:
for intArgs in self.ArgGen(PDFobj,imgprms,mskprms,xydata):
newImage = intArgs[0]
print('processing ',newImage)
ProcessImage(*intArgs)
updateList = True
for newImage in self.currImageList:
self.ProcessedList.append(newImage)
if updateList: self.ShowMatchingFiles(None)
self.PreventTimerReEntry = False
self.Raise()
def ProcessImageMP(onearg):
newImage = onearg[0]
print('processing ',newImage)
t0 = time.time() # debug
ProcessImage(*onearg)
print('ProcessImageMP time',time.time()-t0)
MapCache = {'maskMap':{}, 'ThetaAzimMap':{}, 'distanceList':[]}
'caches for TA and Mask maps'
[docs]
def ProcessImage(newImage,imgprms,mskprms,xydata,PDFdict,InterpVals,calcModes,outputModes):
'''Process one image that is read from file newImage and is integrated into
one or more diffraction patterns and optionally each diffraction pattern can
be transformed into a pair distribution function.
:param str newImage: file name (full path) for input image
:param dict imgprms: dict with some nested lists & dicts describing the image
settings and integration parameters
:param dict mskprms: dict with areas of image to be masked
:param dict xydata: contains histogram information with about background
contributions, used for PDF computation (used if ComputePDF is True)
:param PDFdict: contains PDF parameters (used if ComputePDF is True)
:param InterpVals: contains interpolation table (used if TableMode is True)
:param tuple calcModes: set of values for which computations are
performed and how
:param tuple outputModes: determines which files are written and where
'''
(TableMode,ComputePDF,SeparateDir,optPDF) = calcModes
(outputSelect,PDFformats,fmtlist,outdir,multipleFmtChoices) = outputModes
if SeparateDir:
savedir = os.path.join(outdir,'gpx')
if not os.path.exists(savedir): os.makedirs(savedir)
else:
savedir = outdir
outgpx = os.path.join(savedir,os.path.split(os.path.splitext(newImage)[0]+'.gpx')[1])
gpxout = G2sc.G2Project(filename=outgpx)
print('creating',gpxout.filename)
# looped because a file can contain multiple images
if TableMode: # look up parameter values from table
imgprms,mskprms = LookupFromTable(im.data['Image Controls'].get('setdist'),
InterpVals)
for im in gpxout.add_image(newImage):
# apply image parameters
im.setControls(imgprms)
setdist = '{:.2f}'.format(im.getControls()['setdist']) # ignore differences in position less than 0.01 mm
if setdist not in MapCache['distanceList']:
if mskprms:
im.setMasks(mskprms)
else:
im.initMasks()
MapCache['distanceList'].append(setdist)
MapCache['maskMap'][setdist] = G2sc.calcMaskMap(im.getControls(),
im.getMasks())
MapCache['ThetaAzimMap'][setdist] = G2sc.calcThetaAzimMap(im.getControls())
# else: # debug
# print('*** reusing',setdist)
#if mskprms:
# im.setMasks(mskprms)
#else:
# im.initMasks()
hists = im.Integrate(MaskMap=MapCache['maskMap'][setdist],
ThetaAzimMap=MapCache['ThetaAzimMap'][setdist])
# write requested files
for dfmt in fmtlist:
fmt = dfmt[1:]
if not outputSelect[fmt]: continue
if fmtlist[dfmt] is None: continue
hint = ''
if fmt in multipleFmtChoices:
hint = multipleFmtChoices[fmt]
if SeparateDir:
savedir = os.path.join(outdir,fmt)
else:
savedir = outdir
if not os.path.exists(savedir): os.makedirs(savedir)
# loop over created histgrams (multiple if caked), writing them as requested
for i,h in enumerate(hists):
fname = h.name[5:].replace(' ','_')
#if len(hists) > 1:
#GSASIIpath.IPyBreak_base()
try:
fil = os.path.join(savedir,fname)
print('Wrote',h.Export(fil,dfmt,hint))
except Exception as msg:
print('Failed to write {} as {}. Error msg\n{}'
.format(fname,dfmt,msg))
if ComputePDF: # compute PDF
for h in hists:
pdf = gpxout.copy_PDF(PDFdict,h)
pdf.data['PDF Controls']['Sample']['Name'] = h.name
xydata['Sample'] = h.data['data']
fname = h.name[5:].replace(' ','_')
limits = h.data['Limits'][1]
inst = h.data['Instrument Parameters'][0]
pdf.calculate(copy.deepcopy(xydata),limits,inst)
if optPDF:
for i in range(5):
if pdf.optimize(True,5,copy.deepcopy(xydata),limits,inst):
break
pdf.calculate(copy.deepcopy(xydata),limits,inst)
for fmt in PDFformats:
if not outputSelect[fmt]: continue
if SeparateDir:
savedir = os.path.join(outdir,fmt.replace("(","_").replace(")",""))
else:
savedir = outdir
pdf.export(os.path.join(savedir,fname),fmt)
if outputSelect.get('gpx'):
gpxout.save()
else:
del gpxout
# Autointegration end
[docs]
def SetupInterpolation(dlg):
'''Creates an object for interpolating image parameters at a given distance value
'''
parms = dlg.ReadImageParmTable()
IMfileList = dlg.IMfileList
cols = dlg.list.GetColumnCount()
ParmList = dlg.ParmList
nonInterpVars = dlg.nonInterpVars
ControlsTable = {}
MaskTable = {}
for f,m in zip(IMfileList,parms[-1]):
n = os.path.split(f)[1]
if n in ControlsTable:
print('Warning overwriting entry {}'.format(n))
ControlsTable[n] = G2imG.ReadControls(f)
if m and os.path.exists(m):
MaskTable[n] = G2imG.ReadMask(m)
elif m != "(none)":
print("Error: Mask file {} not found".format(m))
return copy.deepcopy([cols, parms, IMfileList, ParmList, nonInterpVars,ControlsTable,MaskTable])
[docs]
def LookupFromTable(dist,parmList):
'''Interpolate image parameters for a supplied distance value
:param float dist: distance to use for interpolation
:returns: a list with 2 items:
* a dict with interpolated parameter values,
* the closest imctrl
'''
cols, parms, IMfileList, ParmList, nonInterpVars,ControlsTable,MaskTable = parmList
x = np.array([float(i) for i in parms[0]])
closest = abs(x-dist).argmin()
D = {'setdist':dist}
imctfile = IMfileList[closest]
for c in range(1,cols-1):
lbl = ParmList[c]
if lbl in nonInterpVars:
if lbl in ['outChannels',]:
D[lbl] = int(float(parms[c][closest]))
else:
D[lbl] = float(parms[c][closest])
else:
y = np.array([float(i) for i in parms[c]])
D[lbl] = np.interp(dist,x,y)
# full integration when angular range is 0
D['fullIntegrate'] = (D['LRazimuth_min'] == D['LRazimuth_max'])
# conversion for paired values
for a,b in ('center_x','center_y'),('LRazimuth_min','LRazimuth_max'),('IOtth_min','IOtth_max'):
r = a.split('_')[0]
D[r] = [D[a],D[b]]
if r in ['LRazimuth',]:
D[r] = [int(D[a]),int(D[b])]
del D[a]
del D[b]
interpDict,imgctrl = D,imctfile
if GSASIIpath.GetConfigValue('debug'):
print ('DBG_interpolated values: ',interpDict)
f = os.path.split(imgctrl)[1]
ImageControls = ControlsTable[f]
ImageControls.update(interpDict)
ImageControls['showLines'] = True
ImageControls['ring'] = []
ImageControls['rings'] = []
ImageControls['ellipses'] = []
ImageControls['setDefault'] = False
for i in 'range','size','GonioAngles':
if i in ImageControls: del ImageControls[i]
ImageMasks = MaskTable.get(f)
return ImageControls,ImageMasks
###########################################################################
if __name__ == "__main__":
GSASIIpath.InvokeDebugOpts()
App = wx.App()
class dummyClass(object):
'''An empty class where a few values needed from parent are placed
'''
def __init__(self):
self.Image = None
self.PauseIntegration = False
self.TutorialImportDir = None
self.GSASprojectfile = ''
self.LastExportDir = ''
self.LastGPXdir = ''
G2frame = dummyClass()
frm = AutoIntFrame(G2frame,5)
App.GetTopWindow().Show(True)
App.MainLoop()