Changeset 4415 for trunk/GSASIIplot.py


Ignore:
Timestamp:
May 7, 2020 12:17:26 PM (3 years ago)
Author:
vondreele
Message:

change export_PDB to handle fullrmc pdb files
implement Wenqian's mod for the geometric image correction
TransformPhase? & FillUnitCell? now have option to not force atoms to new unit cell (default=True)
refactor FillAtomLookup?
change FindAllNeighbors? to optionally give short output
remove result of double click on Uiso column heading
many additions & changes for fulrmc GUI, etc.
comment out obsolete MPLsubplots from G2plot - no longer needed (pre mpl 2.2)
modify PDB importer to handle fullrmc pdb files.

File:
1 edited

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  • trunk/GSASIIplot.py

    r4408 r4415  
    290290    fil.write(line+'\n')
    291291
    292 def MPLsubplots(figure, nrows=1, ncols=1, sharex=False, sharey=False,
    293                  squeeze=True, subplot_kw=None, gridspec_kw=None):
    294         """
    295         Add a set of subplots to this figure.
    296        
    297         This is a copy of Figure.figure.subplots from matplotlib.figure.py.
    298         Included here because this appears only in later versions of
    299         matplotlib. When v2.2 is standard, this should be removed from GSAS-II.
    300        
    301         :param int nrows, ncols: default: 1
    302             Number of rows/cols of the subplot grid.
    303         :param bool/str sharex, sharey: True/False or {'none', 'all', 'row', 'col'}, default: False
    304 
    305             Controls sharing of properties among x (`sharex`) or y (`sharey`)
    306             axes:
     292# def MPLsubplots(figure, nrows=1, ncols=1, sharex=False, sharey=False,
     293#                  squeeze=True, subplot_kw=None, gridspec_kw=None):
     294#         """
     295#         Add a set of subplots to this figure.
     296       
     297#         This is a copy of Figure.figure.subplots from matplotlib.figure.py.
     298#         Included here because this appears only in later versions of
     299#         matplotlib. When v2.2 is standard, this should be removed from GSAS-II.
     300       
     301#         :param int nrows, ncols: default: 1
     302#             Number of rows/cols of the subplot grid.
     303#         :param bool/str sharex, sharey: True/False or {'none', 'all', 'row', 'col'}, default: False
     304
     305#             Controls sharing of properties among x (`sharex`) or y (`sharey`)
     306#             axes:
    307307           
    308                 - True or 'all': x- or y-axis will be shared among all
    309                   subplots.
    310                 - False or 'none': each subplot x- or y-axis will be
    311                   independent.
    312                 - 'row': each subplot row will share an x- or y-axis.
    313                 - 'col': each subplot column will share an x- or y-axis.
     308#                 - True or 'all': x- or y-axis will be shared among all
     309#                   subplots.
     310#                 - False or 'none': each subplot x- or y-axis will be
     311#                   independent.
     312#                 - 'row': each subplot row will share an x- or y-axis.
     313#                 - 'col': each subplot column will share an x- or y-axis.
    314314               
    315             When subplots have a shared x-axis along a column, only the x tick
    316             labels of the bottom subplot are visible.  Similarly, when
    317             subplots have a shared y-axis along a row, only the y tick labels
    318             of the first column subplot are visible.
    319         :param bool squeeze: default: True
    320 
    321             - If True, extra dimensions are squeezed out from the returned
    322               axis object:
     315#             When subplots have a shared x-axis along a column, only the x tick
     316#             labels of the bottom subplot are visible.  Similarly, when
     317#             subplots have a shared y-axis along a row, only the y tick labels
     318#             of the first column subplot are visible.
     319#         :param bool squeeze: default: True
     320
     321#             - If True, extra dimensions are squeezed out from the returned
     322#               axis object:
    323323             
    324                 - if only one subplot is constructed (nrows=ncols=1), the
    325                   resulting single Axes object is returned as a scalar.
    326                 - for Nx1 or 1xN subplots, the returned object is a 1D numpy
    327                   object array of Axes objects are returned as numpy 1D
    328                   arrays.
    329                 - for NxM, subplots with N>1 and M>1 are returned as a 2D
    330                   arrays.
     324#                 - if only one subplot is constructed (nrows=ncols=1), the
     325#                   resulting single Axes object is returned as a scalar.
     326#                 - for Nx1 or 1xN subplots, the returned object is a 1D numpy
     327#                   object array of Axes objects are returned as numpy 1D
     328#                   arrays.
     329#                 - for NxM, subplots with N>1 and M>1 are returned as a 2D
     330#                   arrays.
    331331                 
    332             - If False, no squeezing at all is done: the returned Axes object
    333               is always a 2D array containing Axes instances, even if it ends
    334               up being 1x1.
     332#             - If False, no squeezing at all is done: the returned Axes object
     333#               is always a 2D array containing Axes instances, even if it ends
     334#               up being 1x1.
    335335             
    336         :param dict subplot_kw: default: {}
    337             Dict with keywords passed to the
    338             :meth:`matplotlib.figure.Figure.add_subplot` call used to create
    339             each subplots.
    340         :param dict gridspec_kw: default: {}
    341             Dict with keywords passed to the
    342             :class:`matplotlib.gridspec.GridSpec` constructor used to create
    343             the grid the subplots are placed on.
     336#         :param dict subplot_kw: default: {}
     337#             Dict with keywords passed to the
     338#             :meth:`matplotlib.figure.Figure.add_subplot` call used to create
     339#             each subplots.
     340#         :param dict gridspec_kw: default: {}
     341#             Dict with keywords passed to the
     342#             :class:`matplotlib.gridspec.GridSpec` constructor used to create
     343#             the grid the subplots are placed on.
    344344           
    345         :returns: A single Axes object or array of Axes objects with
    346             the added axes.  The dimensions of the resulting array can be
    347             controlled with the squeeze keyword, see above.
     345#         :returns: A single Axes object or array of Axes objects with
     346#             the added axes.  The dimensions of the resulting array can be
     347#             controlled with the squeeze keyword, see above.
    348348           
    349         See also: pyplot.subplots: pyplot API; docstring includes examples.
    350        
    351         """
    352 
    353         # for backwards compatibility
    354         if isinstance(sharex, bool):
    355             sharex = "all" if sharex else "none"
    356         if isinstance(sharey, bool):
    357             sharey = "all" if sharey else "none"
    358         share_values = ["all", "row", "col", "none"]
    359         if sharex not in share_values:
    360             # This check was added because it is very easy to type
    361             # `subplots(1, 2, 1)` when `subplot(1, 2, 1)` was intended.
    362             # In most cases, no error will ever occur, but mysterious behavior
    363             # will result because what was intended to be the subplot index is
    364             # instead treated as a bool for sharex.
    365             if isinstance(sharex, int):
    366                 warnings.warn(
    367                     "sharex argument to subplots() was an integer. "
    368                     "Did you intend to use subplot() (without 's')?")
    369 
    370             raise ValueError("sharex [%s] must be one of %s" %
    371                              (sharex, share_values))
    372         if sharey not in share_values:
    373             raise ValueError("sharey [%s] must be one of %s" %
    374                              (sharey, share_values))
    375         if subplot_kw is None:
    376             subplot_kw = {}
    377         if gridspec_kw is None:
    378             gridspec_kw = {}
    379 
    380         # if figure.get_constrained_layout():
    381         #     gs = GridSpec(nrows, ncols, figure=figure, **gridspec_kw)
    382         # else:
    383         #     # this should turn constrained_layout off if we don't want it
    384         #     gs = GridSpec(nrows, ncols, figure=None, **gridspec_kw)
    385         gs = mpl.gridspec.GridSpec(nrows, ncols, **gridspec_kw)
    386 
    387         # Create array to hold all axes.
    388         axarr = np.empty((nrows, ncols), dtype=object)
    389         for row in range(nrows):
    390             for col in range(ncols):
    391                 shared_with = {"none": None, "all": axarr[0, 0],
    392                                "row": axarr[row, 0], "col": axarr[0, col]}
    393                 subplot_kw["sharex"] = shared_with[sharex]
    394                 subplot_kw["sharey"] = shared_with[sharey]
    395                 axarr[row, col] = figure.add_subplot(gs[row, col], **subplot_kw)
    396 
    397         # turn off redundant tick labeling
    398         if sharex in ["col", "all"]:
    399             # turn off all but the bottom row
    400             for ax in axarr[:-1, :].flat:
    401                 ax.xaxis.set_tick_params(which='both',
    402                                          labelbottom=False, labeltop=False)
    403                 ax.xaxis.offsetText.set_visible(False)
    404         if sharey in ["row", "all"]:
    405             # turn off all but the first column
    406             for ax in axarr[:, 1:].flat:
    407                 ax.yaxis.set_tick_params(which='both',
    408                                          labelleft=False, labelright=False)
    409                 ax.yaxis.offsetText.set_visible(False)
    410 
    411         if squeeze:
    412             # Discarding unneeded dimensions that equal 1.  If we only have one
    413             # subplot, just return it instead of a 1-element array.
    414             return axarr.item() if axarr.size == 1 else axarr.squeeze()
    415         else:
    416             # Returned axis array will be always 2-d, even if nrows=ncols=1.
    417             return axarr
     349#         See also: pyplot.subplots: pyplot API; docstring includes examples.
     350       
     351#         """
     352
     353#         # for backwards compatibility
     354#         if isinstance(sharex, bool):
     355#             sharex = "all" if sharex else "none"
     356#         if isinstance(sharey, bool):
     357#             sharey = "all" if sharey else "none"
     358#         share_values = ["all", "row", "col", "none"]
     359#         if sharex not in share_values:
     360#             # This check was added because it is very easy to type
     361#             # `subplots(1, 2, 1)` when `subplot(1, 2, 1)` was intended.
     362#             # In most cases, no error will ever occur, but mysterious behavior
     363#             # will result because what was intended to be the subplot index is
     364#             # instead treated as a bool for sharex.
     365#             if isinstance(sharex, int):
     366#                 warnings.warn(
     367#                     "sharex argument to subplots() was an integer. "
     368#                     "Did you intend to use subplot() (without 's')?")
     369
     370#             raise ValueError("sharex [%s] must be one of %s" %
     371#                              (sharex, share_values))
     372#         if sharey not in share_values:
     373#             raise ValueError("sharey [%s] must be one of %s" %
     374#                              (sharey, share_values))
     375#         if subplot_kw is None:
     376#             subplot_kw = {}
     377#         if gridspec_kw is None:
     378#             gridspec_kw = {}
     379
     380#         # if figure.get_constrained_layout():
     381#         #     gs = GridSpec(nrows, ncols, figure=figure, **gridspec_kw)
     382#         # else:
     383#         #     # this should turn constrained_layout off if we don't want it
     384#         #     gs = GridSpec(nrows, ncols, figure=None, **gridspec_kw)
     385#         gs = mpl.gridspec.GridSpec(nrows, ncols, **gridspec_kw)
     386
     387#         # Create array to hold all axes.
     388#         axarr = np.empty((nrows, ncols), dtype=object)
     389#         for row in range(nrows):
     390#             for col in range(ncols):
     391#                 shared_with = {"none": None, "all": axarr[0, 0],
     392#                                "row": axarr[row, 0], "col": axarr[0, col]}
     393#                 subplot_kw["sharex"] = shared_with[sharex]
     394#                 subplot_kw["sharey"] = shared_with[sharey]
     395#                 axarr[row, col] = figure.add_subplot(gs[row, col], **subplot_kw)
     396
     397#         # turn off redundant tick labeling
     398#         if sharex in ["col", "all"]:
     399#             # turn off all but the bottom row
     400#             for ax in axarr[:-1, :].flat:
     401#                 ax.xaxis.set_tick_params(which='both',
     402#                                          labelbottom=False, labeltop=False)
     403#                 ax.xaxis.offsetText.set_visible(False)
     404#         if sharey in ["row", "all"]:
     405#             # turn off all but the first column
     406#             for ax in axarr[:, 1:].flat:
     407#                 ax.yaxis.set_tick_params(which='both',
     408#                                          labelleft=False, labelright=False)
     409#                 ax.yaxis.offsetText.set_visible(False)
     410
     411#         if squeeze:
     412#             # Discarding unneeded dimensions that equal 1.  If we only have one
     413#             # subplot, just return it instead of a 1-element array.
     414#             return axarr.item() if axarr.size == 1 else axarr.squeeze()
     415#         else:
     416#             # Returned axis array will be always 2-d, even if nrows=ncols=1.
     417#             return axarr
    418418
    419419class _tabPlotWin(wx.Panel):   
    … …  
    29992999        Plot.set_visible(False)         #hide old plot frame, will get replaced below
    30003000        GS_kw = {'height_ratios':[4, 1],}
    3001         try:
    3002             Plot,Plot1 = Page.figure.subplots(2,1,sharex=True,gridspec_kw=GS_kw)
    3003         except AttributeError: # figure.Figure.subplots added in MPL 2.2
    3004             Plot,Plot1 = MPLsubplots(Page.figure, 2, 1, sharex=True, gridspec_kw=GS_kw)
     3001        # try:
     3002        Plot,Plot1 = Page.figure.subplots(2,1,sharex=True,gridspec_kw=GS_kw)
     3003        # except AttributeError: # figure.Figure.subplots added in MPL 2.2
     3004        #     Plot,Plot1 = MPLsubplots(Page.figure, 2, 1, sharex=True, gridspec_kw=GS_kw)
    30053005        Plot1.set_ylabel(r'$\mathsf{\Delta(I)/\sigma(I)}$',fontsize=16)
    30063006        Plot1.set_xlabel(xLabel,fontsize=16)
    … …  
    76427642        Plot.set_visible(False)
    76437643        GS_kw = {'width_ratios':[1,2],}
    7644         try:
    7645             Plot1,Plot = Page.figure.subplots(1,2,gridspec_kw=GS_kw)
    7646         except AttributeError: # figure.Figure.subplots added in MPL 2.2
    7647             Plot1,Plot = MPLsubplots(Page.figure, 1,2, gridspec_kw=GS_kw)
     7644        # try:
     7645        Plot1,Plot = Page.figure.subplots(1,2,gridspec_kw=GS_kw)
     7646        # except AttributeError: # figure.Figure.subplots added in MPL 2.2
     7647        #     Plot1,Plot = MPLsubplots(Page.figure, 1,2, gridspec_kw=GS_kw)
    76487648        Plot1.set_title('Line scan at azm= %6.1f'%Data['linescan'][1])
    76497649        Plot1.set_xlabel(r'$\mathsf{2\Theta}$',fontsize=12)
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