GSAS-II

https://gsas-ii.readthedocs.io/en/latest/
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GSAS-II is an open-source Python package for crystallographic data analysis, structure...
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### Install packages using pip

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html

Examples of passing a list of package names or file paths to the pipInstall function.

```python
packageList=['gsl']
packageList=['wxpython','matplotlib','scipy']
packageList=[r'\Mac\Home\Scratch\wheels\pygsl-2.3.3-py3-none-any.whl']
packageList=['z:/Scratch/wheels/pygsl-2.3.3-py3-none-any.whl']
```

--------------------------------

### Configure SelectEdit1Var parameters

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIIGUIr.html

Example setup for the SelectEdit1Var function, demonstrating how to map data arrays to labels and refinement flags.

```python
 array = data
 labelLst = ['v1','v2']
 elemKeysLst = [['v1'], ['v2',0]]
 refFlgElem = [None, ['v2',1]]

* The value for v1 will be in data['v1'] and this cannot be refined while,
* The value for v2 will be in data['v2'][0] and its refinement flag is data['v2'][1]
```

--------------------------------

### Initialize and Start GSAS-II GUI

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIGUI.html

The main routine handles platform-specific wxPython application setup and invokes the GSAS-II data GUI.

```python
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#GSASIIGUI
'''
GSASIIGUI provides a short file that is used to start the GSAS-II GUI. 
It is usually called from `G2.py` but this routine can also be invoked
directly when GSAS-II has been installed into Python. 
On MacOS, a class, :class:`G2App`, is defined inside :func:`main` that creates
a wxPython application. For other platforms ``wx.App()`` is called directly.
'''

import sys

from . import GSASIIpath

__version__ = '5.0.0'
gv = GSASIIpath.getSavedVersionInfo()
if gv is not None:
    if len(gv.git_versiontag):
        __version__ = gv.git_versiontag[1:]
    elif len(gv.git_tags):
        __version__ = gv.git_tags[0]
    elif len(gv.git_prevtags):
        __version__ = gv.git_prevtags[0]



[docs]
def main():
    '''This routine is called to start the GSAS-II GUI
    '''
    import scipy.optimize # loading here addresses problem with build for wx on Pi
    import wx
    # the next line removes the need for pythonw. Thanks to Matt Newville!
    # appears unneeded from wx 4.2.1 on
    if sys.platform.lower() == 'darwin':
        wx.PyApp.IsDisplayAvailable = lambda _: True
    # importing the following wx modules at the same time as wx seems to
    # eliminate the "Debug: Adding duplicate image handler for 'Windows bitmap
    # file'" error message
    import wx.grid as wg
    import wx.aui
    import wx.lib.scrolledpanel as wxscroll
    import wx.lib.mixins.listctrl  as  listmix
    import wx.richtext as wxrt
    import wx.lib.filebrowsebutton as wxfilebrowse
    wg,wx.aui,wxscroll,listmix,wxrt,wxfilebrowse,scipy.optimize # avoid unused warning

    if sys.platform == "darwin":
        class G2App(wx.App):
            '''Used to create a wx python application for the GUI for Mac.
            Customized to implement drop of GPX files onto app.
            '''
            startupMode = True
            def ClearStartup(self):
                '''Call this after app startup complete because a Drop event is posted
                when GSAS-II is initially started.
                '''
                self.startupMode = False
            def MacOpenFiles(self, filenames):
                if self.startupMode:
                    return
                from . import GSASIIfiles
                for project in filenames:
                    #print("Start GSAS-II with project file "+str(project))
                    #GSASIIpath.MacStartGSASII(__file__,project)
                    GSASIIfiles.openInNewTerm(project)

        application = G2App(0) # create the GUI framework
    else:
        application = wx.App(0) # create the GUI framework
    try:
        GSASIIpath.SetBinaryPath(True)
    except Exception as msg:
        print(
'''Unable to run with current installation due to lack of binary (compiled) 
files, please reset or reinstall''')
        print('\nError:')
        print(msg)
        # if GSASIIpath.HowIsG2Installed().startswith('git'):
        #     print('use this command w/gitstrap')
        
        sys.exit()
        # print('Unable to run with current setup, do you want to update to the')
        # try:
        #     ans = input("latest GSAS-II version? Update ([Yes]/no): ")
        # except:
        #     ans = 'no'
        # if ans.strip().lower() == "no":
        #     import sys
        #     print('Exiting')
        #     sys.exit()
        # print('Updating...')
        # import GSASIIctrlGUI as G2G
        # if GSASIIpath.HowIsG2Installed().startswith('git'):
        #     gitCheckUpdates(None)
    from . import GSASIIdataGUI as G2gd
    GSASIIpath.InvokeDebugOpts()
    # debug capability. If a Python file is on the command-line import it
    if GSASIIpath.GetConfigValue('debug') and len(sys.argv) == 2:
        import os
        if os.path.splitext(sys.argv[1])[1] == '.py':
            print (f'{60*"="}\n"Importing" file {sys.argv[1]}\n{60*"="}')
            import importlib.util
            spec = importlib.util.spec_from_file_location('test_module', sys.argv[1])
            module = importlib.util.module_from_spec(spec)
            sys.modules['test_module'] = module
            spec.loader.exec_module(module)
            #test_module = module
            sys.exit()
    G2gd.GSASIImain(application) # start the GUI
    if sys.platform == "darwin":
        wx.CallLater(50,application.ClearStartup)
    application.MainLoop()



if __name__ == '__main__':
    main()
```

--------------------------------

### Start GSAS-II GUI via Command Line

Source: https://gsas-ii.readthedocs.io/en/latest/GSASII.html

Use this command to launch the GSAS-II GUI when the installation directory is already in the Python path.

```bash
python -c “from GSASII.GSASIIGUI import main; main()”
```

--------------------------------

### main(application)

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/G2compare.html

Initializes and starts the GSAS-II Compare GUI application.

```APIDOC
## main(application)

### Description
Starts up the GSAS-II Compare GUI. It validates the Python environment version and initializes the main window.

### Parameters
- **application** (object) - The application instance to be initialized.

### Returns
- (wx.Frame) The main top-level window of the application.
```

--------------------------------

### Install Miniconda and Dependencies

Source: https://gsas-ii.readthedocs.io/en/latest/packages.html

Commands to install Miniconda, activate the environment, and install required Python packages.

```bash
bash ~/Downloads/Miniconda3-latest-<platform>-x86_64.sh -b -p /loc/pyg2script
source /loc/pyg2script/bin/activate
conda install numpy scipy pycifrw matplotlib-base pillow h5py hdf5
```

--------------------------------

### Install packages with condaInstall

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html

Examples of passing package lists and optional conda flags to the condaInstall function.

```python
packageList=['gsl']
packageList=['-c','conda-forge','wxpython']
packageList=['numpy','scipy','matplotlib']
```

--------------------------------

### GSASII.GSASIIElem.SetupGeneral

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html

Initializes the General sections of the Phase tree.

```APIDOC
## GSASII.GSASIIElem.SetupGeneral(data, dirname)

### Description
Initializes the General sections of the Phase tree contents. Should be executed after changes to the Atoms array.
```

--------------------------------

### Get Repository Updates in Background

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIpath.html

Checks if GSAS-II is installed via Git and triggers a background update process.

```python
def GetRepoUpdatesInBackground():
    '''Get the latest GSAS-II version info.
    This serves to make sure that :func:`gitGetUpdate` is called only
    if git has been used to install GSAS-II.

    :returns: returns a Popen object (see subprocess)
    '''
    if HowIsG2Installed().startswith('git'):
        return gitGetUpdate(mode='Background')
    else:
        return saveGitHubVersion()
```

--------------------------------

### Initialize Origin Instance and Data Folders

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIpwdplot.html

Sets up the Origin application instance and creates a dedicated folder for the refinement data.

```python
# Start Origin instance
        if op and op.oext:
            sys.excepthook = origin_shutdown_exception_hook

        # Set Origin instance visibility
        if op.oext:
            op.set_show(True)
        op.new()

        # Create folder to hold data and graph
        refinementName = G2frame.Label
        refinementName = refinementName[17:-4]
        fldr = op.po.RootFolder.Folders.Add(refinementName)
        fldr.Activate()
```

--------------------------------

### Setup sequential refinement

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIIscriptable.html

Initializes paths and helper functions for setting up a sequential refinement workflow.

```python
import os,glob
datadir = os.path.expanduser("~/Scratch/SeqTut2019Mar")
PathWrap = lambda fil: os.path.join(datadir,fil)
```

--------------------------------

### Get Current Git Branch

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIpath.html

Retrieves the name of the active Git branch for the GSAS-II installation, returning '?' if in a detached head state.

```python
[docs]
def getG2Branch():
    '''Get name of current branch, as named on local computer
    '''
    if HowIsG2Installed().startswith('git'):
        g2repo = openGitRepo(path2GSAS2)
        try:
            return g2repo.active_branch.name
        except TypeError: # likely on a detached head
            return '?'
```

--------------------------------

### Initialize GUI Layout

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIIntPDFtool.html

Sets up the bottom button sizer, core count spin control, and initial window configuration.

```python
# 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)
```

--------------------------------

### Initialize Integration Output GUI

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIIntPDFtool.html

Sets up the static box and sizers for integration output, including directory selection and format checkboxes.

```python
# 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_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)
```

--------------------------------

### G2Image Usage Example

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIIscriptable.html

Demonstrates initializing a project, adding an image, and performing common image processing tasks like calibration and integration.

```python
>>> gpx = G2sc.G2Project(newgpx='itest.gpx')
>>> imlst = gpx.add_image(idata,fmthint="TIF")
>>> imlst[0].loadControls('stdSettings.imctrl')
>>> imlst[0].setCalibrant('Si    SRM640c')
>>> imlst[0].loadMasks('stdMasks.immask')
>>> imlst[0].Recalibrate()
>>> imlst[0].setControl('outAzimuths',3)
>>> pwdrList = imlst[0].Integrate()
```

--------------------------------

### Configure Tutorial Location

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html

Sets the directory path for tutorial files.

```python
Tutorial_location = GSASIIpath.path2GSAS2
```

```python
Tutorial_location = '~/.G2tutorials'
```

--------------------------------

### Install packages using pip

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIpath.html

Installs packages using the pip installer. It automatically converts conda-style package specifiers to pip-compatible format.

```python
def pipInstall(packageList):
    '''Installs one or more packages using the pip package installer.
    Use of this should be avoided if conda can be used (see :func:`condaTest`
    to test for conda). Can be used to install multiple packages together.
    One can use pip options, but this is probably not needed.

    :param list packageList: a list of strings with name(s) of packages
      Examples::

       packageList=['gsl']
       packageList=['wxpython','matplotlib','scipy']
       packageList=[r'\\Mac\\Home\\Scratch\\wheels\\pygsl-2.3.3-py3-none-any.whl']
       packageList=['z:/Scratch/wheels/pygsl-2.3.3-py3-none-any.whl']

    :returns: None if the the command ran normally, or an error message
      if it did not.
    '''
    # update conda package specs (pkg=1.2.3) to pip package specs (pkg==1.2.3)
    # at present no other specifiers are used. 
    for i,val in enumerate(packageList):
        if '=' in val and '==' not in val:
            packageList[i] = packageList[i].replace('=','==')
    try:
        subprocess.check_call([sys.executable, '-m', 'pip', 'install']+packageList)
    except Exception as msg:
        return msg
    return None
```

--------------------------------

### GSASII.GSASIIpath.pipInstall()

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html

Installs one or more packages using the pip package installer.

```APIDOC
## GSASII.GSASIIpath.pipInstall(packageList)

### Description
Installs one or more packages using the pip package installer. Use of this should be avoided if conda can be used.

### Parameters
- **packageList** (list) - Required. A list of strings with name(s) of packages to install.

### Returns
- **None/string** - None if the command ran normally, or an error message if it did not.
```

--------------------------------

### Initialize testSytSym GUI

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/testSytSym.html

Setup script for the testSytSym module, including environment path configuration and wxPython frame initialization.

```python
#testMagSym
import sys
import os
import wx
import numpy as np
import importlib.util
try:
    importlib.util.find_spec('GSASII.GSASIIGUI')
except ModuleNotFoundError:
    print('GSAS-II not installed in Python; Hacking sys.path')
    sys.path.insert(0,os.path.dirname(os.path.dirname(__file__)))
from GSASII import GSASIIpath
GSASIIpath.SetBinaryPath()
from GSASII import GSASIIspc as G2spc
from GSASII import GSASIIlattice as G2lat
from GSASII import GSASIIctrlGUI as G2G
from GSASII import GSASIIphsGUI as G2phsGUI

try:
    wx.NewId
except AttributeError:
    wx.NewId = wx.NewIdRef
    
[wxID_FILEEXIT, 
] = [wx.NewId() for _init_coll_File_Items in range(1)]
WACV = wx.ALIGN_CENTER_VERTICAL


[docs]
class testSytSym(wx.Frame):

    def _init_ctrls(self, parent):
        wx.Frame.__init__(self, name='testSytSym', parent=parent,
            size=[800,300],style=wx.DEFAULT_FRAME_STYLE, title='Test space group site symmetry')
        self.testSSMenu = wx.MenuBar()
        self.File = wx.Menu(title='')
        self.File.Append(wxID_FILEEXIT,'Exit')
        self.Bind(wx.EVT_MENU, self.OnFileExit, id=wxID_FILEEXIT)
        self.testSSMenu.Append(menu=self.File, title='Run')
        self.SetMenuBar(self.testSSMenu)
        self.testSSPanel = wx.Window(self)        
        
    def __init__(self, parent):
        self._init_ctrls(parent)
        self.Bind(wx.EVT_CLOSE, self.ExitMain)    
        self.dataFrame = None
        Data = {'SGData':G2spc.SpcGroup('P 1')[1],}
        self.RBsym = '1'
        self.propVec = '0,0,0'
        self.XYZ = '0,0,0'
        self.UpdateData(Data)
```

--------------------------------

### Initialize Tool State

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIIntPDFtool.html

Sets up initial parameters, timers, and file format lists for the tool instance.

```python
        ##################################################
        # 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
```

--------------------------------

### Equivalence Definition Example

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIImapvars.html

Example syntax for defining parameter equivalences.

```text
::x1 -> ::x2 & ::x4
```

--------------------------------

### pipInstall(packageList)

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIpath.html

Installs one or more packages using the pip package installer.

```APIDOC
## pipInstall(packageList)

### Description
Installs one or more packages using the pip package installer. It automatically converts conda-style package specifiers (e.g., pkg=1.2.3) to pip-style (pkg==1.2.3).

### Parameters
- **packageList** (list) - A list of strings containing the names of packages to install.

### Returns
- **None** - If the command ran normally.
- **str/Exception** - An error message or exception if the installation failed.
```

--------------------------------

### Initialize G2Project

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIIscriptable.html

Demonstrates how to initialize a G2Project object by either loading an existing file or creating a new one.

```python
>>> # Load an existing project file
>>> proj = G2Project('filename.gpx')
```

```python
>>> # Create a new project
>>> proj = G2Project(newgpx='new_file.gpx')
```

--------------------------------

### HowIsG2Installed()

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIpath.html

Determines if GSAS-II was installed via git and returns the installation type.

```APIDOC
## HowIsG2Installed

### Description
Determines if GSAS-II was installed with git. The result is cached to optimize performance for multiple calls.

### Returns
- **str** - Returns 'github' (with optional '-rev' suffix) if installed from the GSAS-II GitHub repository, or 'noVCS' if installed without a version control system.
```

--------------------------------

### GSASII.GSASIIctrlGUI.GSGrid.setupPopup

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIIGUIr.html

Defines a callback that creates a popup menu for the grid.

```APIDOC
## setupPopup(lblList, callList)

### Description
Creates a popup menu where selecting an item triggers a corresponding function call.

### Parameters
- **lblList** (list) - Required - List of string items for the popup menu.
- **callList** (list) - Required - List of functions to be called when a menu item is selected.

### Returns
- **callback** (function) - A callback that can be used to create the menu.
```

--------------------------------

### Install GSAS-II binary files

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIpath.html

Installs GSAS-II binary files into a specified directory.

```python
[docs]
def InstallGitBinary(tarURL, instDir, nameByVersion=False, verbose=True):
    '''Install the GSAS-II binary files into the location
    specified.

```

--------------------------------

### Setup Parameter Dictionary

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIrestrGUI.html

Creates a dictionary mapping variable names to their current numerical values.

```python
    def SetupParmDict(G2frame):
        '''Creates a parameter dict with variable names as keys and 
        numerical values (only)
        '''
        G2cnstG.CheckAllScalePhaseFractions(G2frame,refine=False)
        try:
            parmDict,varyList = G2frame.MakeLSParmDict()
        except:
            print('Error retrieving parameters')
            return {}
        return {i:parmDict[i][0] for i in parmDict}
```

--------------------------------

### Export installed packages from environment

Source: https://gsas-ii.readthedocs.io/en/latest/packages.html

Lists packages explicitly installed in a specific Conda environment.

```bash
conda env export --from-history -n <env>
```

--------------------------------

### Initialize Frame Controls

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/Absorb.html

Sets up the main frame, menu bar, and initial panel drawing.

```python
    def _init_ctrls(self, parent):
        wx.Frame.__init__(self, parent=parent,
              size=wx.Size(500, 400),style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX, title='Absorb')
        self._init_utils()
        self.SetMenuBar(self.menuBar1)
        self.DrawPanel()
```

--------------------------------

### Chained Equivalence Example

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIImapvars.html

Example of chained equivalences where a parameter acts as both a dependent and independent variable.

```text
C1 * P1 = C2 * P2
C2 * P2 = C3 * P3
```

--------------------------------

### Example of a single calibrant entry

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIIdata.html

A standard example of a single material entry in the ImageCalibrants dictionary.

```python
'LaB6  SRM660a':([2,],['',][(4.1569162,4.1569162,4.1569162,90,90,90),],0,(1.0,10,10.)),
```

--------------------------------

### Initialize Fprime Utilities

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/fprime.html

Sets up the menu bar and individual menus for the Fprime utility.

```python
def _init_utils(self):
        self.FPRIME = wx.Menu(title='')

        self.KALPHA = wx.Menu(title='')
        self.KALPHA.SetEvtHandlerEnabled(True)

        self.ABOUT = wx.Menu(title='')

        self.menuBar1 = wx.MenuBar()

        self._init_coll_FPRIME_Items(self.FPRIME)
        self._init_coll_KALPHA_Items(self.KALPHA)
        self._init_coll_ABOUT_Items(self.ABOUT)
        self._init_coll_menuBar1_Menus(self.menuBar1)
```

--------------------------------

### Install Conda Package

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIpath.html

Installs the conda API into the current environment using command line tools.

```python
def addCondaPkg():
    '''Install the conda API into the current conda environment using the
    command line, so that the API can be used in the current Python interpreter

    Attempts to do this without a shell failed on the Mac because it seems that
    the environment was inherited; seems to work w/o shell on Windows.
    '''
    if not any([(i in os.environ) for i in ('CONDA_DEFAULT_ENV','CONDA_EXE',
                        'CONDA_PREFIX', 'CONDA_PYTHON_EXE')]):
        return None
    #condaexe = os.environ['CONDA_EXE']
    currenv = os.environ['CONDA_DEFAULT_ENV']
    if sys.platform == "win32":
        cmd = [os.environ['CONDA_EXE'],'install','conda','-n',currenv,'-y']
        with subprocess.Popen(cmd,
                         #stdout=subprocess.PIPE,
                         stderr=subprocess.PIPE,
                         encoding='UTF-8') as p:
            out,err = p.communicate()
    else:
        script = 'source ' + os.path.join(
            os.path.dirname(os.environ['CONDA_PYTHON_EXE']),
            'activate') + ' base; '
        script += 'conda install conda -n '+currenv+' -y'
        with subprocess.Popen(script,shell=True,env={},
                         #stdout=subprocess.PIPE,
                         stderr=subprocess.PIPE,
                         encoding='UTF-8') as p:
            out,err = p.communicate()
    
    if out is not None and GetConfigValue('debug'): print('Output from adding conda:\n',out)
    if err and err is not None:
        print('Note error/warning from running conda:\n',err)
    if currenv == "base":
        print('\nUnexpected action: adding conda to base environment???')
```

--------------------------------

### Initialize Help Dialog

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIpwdplot.html

Sets up a help button with context-specific information for plot export options.

```python
    helpinfo = '''----   Help on creating hard copy   ----
    Select options such as the size of text and colors for plot contents here.
    
    Tricks:
    * Use a color of pure white to remove an element from the plot (light
    gray is plotted)
    * LaTeX-like coding can be used for phase labels such as
    $\rm FeO_2$ (for a subscript 2) or $\gamma$-Ti for a Greek "gamma"
    
    Note that the dpi value is ignored for svg and pdf files, which are
    drawn with vector graphics (infinite resolution). Likewise, the agr and 
    itx options create input files for programs Grace (QtGrace) and Igor 
    Pro, that largely duplicate the displayed plot. Once read into Grace
    or Igor the graphs can then be customized.
    '''
    if sys.platform == "win32":
        helpinfo += '''
Note that the OriginPro connection export requires Origin 2021 or later.'''
    hlp = G2G.HelpButton(dlg,helpinfo)
    sizebox.Add(hlp,0,wx.ALL)
    vbox.Add(sizebox,0,wx.ALL|wx.EXPAND)
```

--------------------------------

### GSASII.GSASIIimgGUI.initPhaseOpts

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIIGUI.html

Ensures that the options for display of partials are all defined.

```APIDOC
## GSASII.GSASIIimgGUI.initPhaseOpts(_phases_)

### Description
Make sure that the options for display of partials are all defined.
```

--------------------------------

### Define Excluded Regions Examples

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIIscriptable.html

Examples of defining excluded regions for histograms using lists of pairs.

```python
[[4.5, 5.5], [8.0, 9.0]]
```

```python
[[130000.0, 140000.0], [160000.0, 170000.0]]
```

```python
[]
```

--------------------------------

### Initialize MakeTopWindow Class

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/G2compare.html

The constructor sets up the main frame, plot window, menu bar, and the split-window interface for the comparison tool.

```python
class MakeTopWindow(wx.Frame):
    '''Define the main frame and its associated menu items
    '''
    def __init__(self, parent):
        size = wx.Size(700,450)
        wx.Frame.__init__(self, name='dComp', parent=parent,
            size=size,style=wx.DEFAULT_FRAME_STYLE, title='GSAS-II data/model comparison')
        # misc vars
        self.VcovColor = 'RdYlGn'
        # plot window
        try:
            size = GSASIIpath.GetConfigValue('Plot_Size')
            if type(size) is tuple:
                pass
            elif type(size) is str:
                size = eval(size)
            else:
                raise Exception
        except:
            size = wx.Size(700,600)
        self.plotFrame = wx.Frame(None,-1,'dComp Plots',size=size,
            style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX)
        self.G2plotNB = G2plt.G2PlotNoteBook(self.plotFrame,G2frame=self)
        #self.plotFrame.Show()
        self.plotFrame.Show(False)  # until we have some graphics, hide the plot window
        # menus
        Frame = self.GetTopLevelParent() # same as self
        self.MenuBar = wx.MenuBar()
        File = wx.Menu(title='')
        self.MenuBar.Append(menu=File, title='&File')
        item = File.Append(wx.ID_ANY,'&Import single project...\tCtrl+O','Open a GSAS-II project file (*.gpx)')
        self.Bind(wx.EVT_MENU, self.onLoadGPX, id=item.GetId())
        item = File.Append(wx.ID_ANY,'&Import multiple projects...\tCtrl+U','Open a GSAS-II project file (*.gpx)')
        self.Bind(wx.EVT_MENU, self.onLoadMultGPX, id=item.GetId())
        item = File.Append(wx.ID_ANY,'&Wildcard import of projects...\tCtrl+W','Open a GSAS-II project file (*.gpx)')
        self.Bind(wx.EVT_MENU, self.onLoadWildGPX, id=item.GetId())
#        item = File.Append(wx.ID_ANY,'&Import selected...','Open a GSAS-II project file (*.gpx)')
#        self.Bind(wx.EVT_MENU, self.onLoadSel, id=item.GetId())

        self.Mode = wx.Menu(title='')
        self.MenuBar.Append(menu=self.Mode, title='&Mode')
        self.wxID_Mode = {}
        for i,m in enumerate(("Histogram","Phase","Project")):
            self.wxID_Mode[m] = i+1
            item = self.Mode.AppendRadioItem(i+1,m+'\tCtrl+{}'.format(i+1),
                                                 'Display {}s'.format(m))
            self.Bind(wx.EVT_MENU, self.onRefresh, id=item.GetId())
        self.hFilter = self.Mode.Append(wx.ID_ANY,'Filter by histogram\tCtrl+F','Only show selected histograms')
        self.Bind(wx.EVT_MENU, self.onHistFilter, id=self.hFilter.GetId())
        modeMenu = wx.Menu(title='')
        self.MenuBar.Append(menu=modeMenu, title='TBD')
        self.modeMenuPos = self.MenuBar.FindMenu('TBD')

        Frame.SetMenuBar(self.MenuBar)
        # status bar
        self.Status = self.CreateStatusBar()
        self.Status.SetFieldsCount(2)
        # split the frame and add the tree
        self.mainPanel = wx.SplitterWindow(self, wx.ID_ANY, style=wx.SP_LIVE_UPDATE|wx.SP_3D)
        self.mainPanel.SetMinimumPaneSize(100)
        self.treePanel = wx.Panel(self.mainPanel, wx.ID_ANY,
            style = wx.TAB_TRAVERSAL|wx.SUNKEN_BORDER)

#        self.dataWindow = G2DataWindow(self.mainPanel)
        self.dataWindow = wx.ScrolledWindow(self.mainPanel)
        dataSizer = wx.BoxSizer(wx.VERTICAL)
        self.dataWindow.SetSizer(dataSizer)
        self.mainPanel.SplitVertically(self.treePanel, self.dataWindow, 200)
        self.Status.SetStatusWidths([200,-1])   # make these match?

        treeSizer = wx.BoxSizer(wx.VERTICAL)
        self.treePanel.SetSizer(treeSizer)
        self.GPXtree = G2G.G2TreeCtrl(id=wx.ID_ANY,
            parent=self.treePanel, size=self.treePanel.GetClientSize(),style=wx.TR_DEFAULT_STYLE )
        #TreeId = self.GPXtree.Id

        treeSizer.Add(self.GPXtree,1,wx.EXPAND|wx.ALL,0)
        #self.GPXtree.Bind(wx.EVT_TREE_SEL_CHANGED,self.OnDataTreeSelChanged)
        self.GPXtree.Bind(wx.EVT_TREE_SEL_CHANGED,self.OnDataTreeSelChanged)
        # self.GPXtree.Bind(wx.EVT_TREE_ITEM_RIGHT_CLICK,self.OnDataTreeSelChanged)
        # self.GPXtree.Bind(wx.EVT_TREE_ITEM_COLLAPSED,
        #     self.OnGPXtreeItemCollapsed, id=TreeId)
        #self.GPXtree.Bind(wx.EVT_TREE_ITEM_EXPANDED,
        #     self.OnGPXtreeItemExpanded, id=TreeId)
        # self.GPXtree.Bind(wx.EVT_TREE_DELETE_ITEM,
        #     self.OnGPXtreeItemDelete, id=TreeId)
        # self.GPXtree.Bind(wx.EVT_TREE_KEY_DOWN,
        #     self.OnGPXtreeKeyDown, id=TreeId)
        # self.GPXtree.Bind(wx.EVT_TREE_BEGIN_RDRAG,
        #     self.OnGPXtreeBeginRDrag, id=TreeId)
        # self.GPXtree.Bind(wx.EVT_TREE_END_DRAG,
        #     self.OnGPXtreeEndDrag, id=TreeId)
        self.root = self.GPXtree.root
        self.Bind(wx.EVT_CLOSE, lambda event: sys.exit())
```

--------------------------------

### Example of a calibrant with absent reflections

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIIdata.html

An example showing how to specify indices of lines that have no intensity despite being allowed.

```python
'Si':([0,],['F d 3 m'],[(5.4311946,5.4311946,5.4311946,90,90,90),],0,(1.,10,10.),(3,10,13,20,23,26,33,35,40,43)),
```

--------------------------------

### Atom Modulation Wave GUI Setup

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIphsGUI2.html

This code snippet handles the initialization of the atom selection interface and the dynamic generation of sizers for modulation wave parameters.

```python
        iatm = atNames.index(G2frame.atmSel)
        atm = atomData[iatm]
        G2elem.AddWave2atm(atm)
        xyz = atm[cx:cx+3]
        atomSizer = wx.BoxSizer(wx.VERTICAL)
        G2G.HorizontalLine(atomSizer,waveData)
        atomSizer.Add(AtomSizer(atm))
        for Stype in ['Sfrac','Spos','Sadp','Smag']:
            if atm[cia] != 'A' and Stype == 'Sadp':    #Uiso can't have modulations! (why not?)
                continue
            if generalData['Type'] != 'magnetic' and Stype == 'Smag':
                break
            try:
                atomSizer.Add(WaveSizer(iatm,atm[-1]['SS1'][Stype],Stype,typeNames[Stype],Labels[Stype]))
            except TypeError:  # not expected anymore
                atomSizer.Add(wx.StaticText(waveData,label='     Error: could not process SS info for this atom'))
                break
        return atomSizer
    
    generalData = data['General']
    cx,ct,cs,cia = generalData['AtomPtrs']
    typeNames = {'Sfrac':' Site fraction','Spos':' Position','Sadp':' Thermal motion','Smag':' Magnetic moment'}
    numVals = {'Sfrac':2,'Spos':6,'Sadp':12,'Smag':6,'ZigZag':5,'Block':5,'Crenel':2}
    posNames = ['Xsin','Ysin','Zsin','Xcos','Ycos','Zcos','Tmin','Tmax','Xmax','Ymax','Zmax']
    adpNames = ['U11sin','U22sin','U33sin','U12sin','U13sin','U23sin',
        'U11cos','U22cos','U33cos','U12cos','U13cos','U23cos']
    magNames = ['MXsin','MYsin','MZsin','MXcos','MYcos','MZcos']
    fracNames = ['Fsin','Fcos','Fzero','Fwid']
    waveTypes = {'Sfrac':['Fourier','Crenel'],'Spos':['Fourier','ZigZag','Block',],'Sadp':['Fourier',],'Smag':['Fourier',]}
    Labels = {'Spos':posNames,'Sfrac':fracNames,'Sadp':adpNames,'Smag':magNames}
    Indx = {}
    waveData = G2frame.waveData
    G2frame.GetStatusBar().SetStatusText('',1)
    generalData = data['General']
    SGData = generalData['SGData']
    SSGData = generalData['SSGData']
    cx,ct,cs,cia = generalData['AtomPtrs']
    atomData = data['Atoms']
    D4Map = generalData.get('4DmapData',{'rho':[]})
    if waveData.GetSizer():
        waveData.GetSizer().Clear(True)
    mainSizer = wx.BoxSizer(wx.VERTICAL)
    mainSizer.Add(wx.StaticText(waveData,label=' Incommensurate propagation wave data'))
    atNames = []
    for atm in atomData:
        atNames.append(atm[ct-1])
    if not atNames:
        mainSizer.Add(wx.StaticText(waveData,label='   (no atoms in phase)'))
        G2phsG.SetPhaseWindow(G2frame.waveData,mainSizer,Scroll=Scroll)
        return
    if G2frame.atmSel not in atNames:
        G2frame.atmSel = atNames[0]

    topSizer = wx.BoxSizer(wx.HORIZONTAL)
    mainSizer.Add(topSizer,0)
    topSizer.Add(wx.StaticText(waveData,label=' Select atom to edit: '),0,WACV)
    atms = wx.ComboBox(waveData,value=G2frame.atmSel,choices=atNames,
        style=wx.CB_READONLY|wx.CB_DROPDOWN)
    atms.Bind(wx.EVT_COMBOBOX,OnAtmSel)
    topSizer.Add(atms,0)
    G2frame.bottomSizer = ShowAtomInfo()
    mainSizer.Add(G2frame.bottomSizer)
    G2phsG.SetPhaseWindow(G2frame.waveData,mainSizer,Scroll=Scroll)
```

--------------------------------

### Import GSASIIscriptable when installed in Python

Source: https://gsas-ii.readthedocs.io/en/latest/GSASIIscriptable.html

Use this import statement when GSAS-II is already installed within the Python environment.

```python
from GSASII import GSASIIscriptable as G2sc
```

--------------------------------

### findConda()

Source: https://gsas-ii.readthedocs.io/en/latest/_modules/GSASII/GSASIIpath.html

Determines if GSAS-II has been installed as g2conda or gsas2full by locating the conda executable and activation script relative to the installation path.

```APIDOC
## findConda()

### Description
Determines if GSAS-II has been installed as g2conda or gsas2full with conda located relative to the file path. It returns the paths to the conda executable and the activation script if found, otherwise returns None.

### Returns
- **tuple** (conda_path, activate_path) - The paths to the conda executable and activation script.
- **None** - If the paths cannot be determined.
```
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