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Bugs from Ivo: scripting & seq. table plotting; script addition for image integration
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1	#!/usr/bin/env python
2	# -- coding: utf-8 --
3	########### SVN repository information ###################
4	# $Date: 2019-05-06 21:16:16 +0000 (Mon, 06 May 2019) $
5	# $Author: vondreele $
6	# $Revision: 3959 $
7	# $URL: trunk/GSASIIscriptable.py $
8	# $Id: GSASIIscriptable.py 3959 2019-05-06 21:16:16Z vondreele $
9	########### SVN repository information ###################
10	#
11	"""
12	GSASIIscriptable: Scripting Interface
13	=======================================
14
15	Routines to use an increasing amount of GSAS-II's capabilities from scripts,
16	without use of the graphical user interface (GUI). GSASIIscriptable can create and access
17	GSAS-II project (.gpx) files and can directly perform image handling and refinements.
18	The module defines wrapper classes (inheriting from :class:`G2ObjectWrapper`) for a growing number
19	of data tree items.
20
21	GSASIIscriptable can be used in two ways. It offers a command-line mode
22	(see :ref:`CommandlineInterface`) that
23	provides access a number of features without writing Python scripts
24	via shell/batch commands. The more powerful mode of GSASIIscriptable is
25	use is through Python scripts that
26	call the module's application interface (API), see API summary that follows or the :ref:`API`
27	section.
28
29	==================================================
30	Application Interface (API) Summary
31	==================================================
32	This section of the documentation provides an overview to API, with full documentation
33	in the :ref:`API` section. The typical API use will be with a Python script, such as this:
34
35	.. code-block:: python
36
37	from __future__ import division, print_function
38	import os,sys
39	sys.path.insert(0,'/Users/toby/software/G2/GSASII') # needed to "find" GSAS-II modules
40	import GSASIIscriptable as G2sc
41	datadir = "/Users/Scratch/"
42	gpx = G2sc.G2Project(os.path.join(datadir,'test2.gpx'))
43	gpx.histogram(0).add_back_peak(4.5,30000,5000,0)
44	pardict = {'set': {'Sample Parameters': ['Absorption', 'Contrast', 'DisplaceX'],
45	'Background': {'type': 'chebyschev', 'refine': True,
46	'peaks':[[0,True]]}}}
47	gpx.set_refinement(pardict)
48
49	GSASIIscriptable can be used to setup and start sequential refinements. This script
50	is used to take the single-dataset fit at the end of Step 1 of the
51	`Sequential Refinement tutorial <https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SeqRefine/SequentialTutorial.htm>`
52	and turn off refinement flags, add histograms and setup the sequential fit, which is then run:
53
54	.. code-block:: python
55
56	import os,sys,glob
57	sys.path.insert(0,'/Users/toby/software/G2/GSASII')
58	import GSASIIscriptable as G2sc
59	datadir = os.path.expanduser("~/Scratch/SeqTut2019Mar")
60	PathWrap = lambda fil: os.path.join(datadir,fil)
61	# load and rename project
62	gpx = G2sc.G2Project(PathWrap('7Konly.gpx'))
63	gpx.save(PathWrap('SeqRef.gpx'))
64	# turn off some variables; turn on Dijs
65	for p in gpx.phases():
66	p.set_refinements({"Cell": False})
67	gpx.phase(0).set_HAP_refinements(
68	{'Scale': False,
69	"Size": {'type':'isotropic', 'refine': False},
70	"Mustrain": {'type':'uniaxial', 'refine': False},
71	"HStrain":True,})
72	gpx.phase(1).set_HAP_refinements({'Scale': False})
73	gpx.histogram(0).clear_refinements({'Background':False,
74	'Sample Parameters':['DisplaceX'],})
75	gpx.histogram(0).ref_back_peak(0,[])
76	gpx.phase(1).set_HAP_refinements({"HStrain":(1,1,1,0)})
77	for fil in sorted(glob.glob(PathWrap('*.fxye'))): # load in remaining fxye files
78	if '00' in fil: continue
79	gpx.add_powder_histogram(fil, PathWrap('OH_00.prm'), fmthint="GSAS powder",phases='all')
80	# copy HAP values, background, instrument params. & limits, not sample params.
81	gpx.copyHistParms(0,'all',['b','i','l'])
82	for p in gpx.phases(): p.copyHAPvalues(0,'all')
83	# setup and launch sequential fit
84	gpx.set_Controls('sequential',gpx.histograms())
85	gpx.set_Controls('cycles',10)
86	gpx.set_Controls('seqCopy',True)
87	gpx.refine()
88
89	Most functionality is provided via the objects and methods described in this section.
90
91	---------------------
92	:class:`G2Project`
93	---------------------
94
95	All GSASIIscriptable scripts will need to create a :class:`G2Project` object
96	either for a new GSAS-II project or to read in an existing project (.gpx) file.
97	The most commonly used routines in this object are:
98
99	.. tabularcolumns:: \|l\|p{3.5in}\|
100
101	================================================== ===============================================================================================================
102	method Use
103	================================================== ===============================================================================================================
104	:meth:`G2Project.save` Writes the current project to disk.
105
106	:meth:`G2Project.add_powder_histogram` Used to read in powder diffraction data into a project file.
107
108	:meth:`G2Project.add_simulated_powder_histogram` Defines a "dummy" powder diffraction data that will be simulated after a refinement step.
109
110	:meth:`G2Project.add_image` Reads in an image into a project.
111
112	:meth:`G2Project.add_phase` Adds a phase to a project
113
114	:meth:`G2Project.histograms` Provides a list of histograms in the current project, as :class:`G2PwdrData` objects
115
116	:meth:`G2Project.phases` Provides a list of phases defined in the current project, as :class:`G2Phase` objects
117
118	:meth:`G2Project.images` Provides a list of images in the current project, as :class:`G2Image` objects
119
120	:meth:`G2Project.do_refinements` This is passed a list of dictionaries, where each dict defines a refinement step.
121	Passing a list with a single empty dict initiates a refinement with the current
122	parameters and flags. A refinement dict sets up a single refinement step
123	(as described in :ref:`Project_dicts`). Also see :ref:`Refinement_recipe`.
124
125	:meth:`G2Project.set_refinement` This is passed a single dict which is used to set parameters and flags.
126	These actions can be performed also in :meth:`G2Project.do_refinements`.
127	================================================== ===============================================================================================================
128
129	---------------------
130	:class:`G2Phase`
131	---------------------
132
133	Another common object in GSASIIscriptable scripts is :class:`G2Phase`, used to encapsulate each phase in a project, with commonly used methods:
134
135	.. tabularcolumns:: \|l\|p{3.5in}\|
136
137	================================================== ===============================================================================================================
138	method Use
139	================================================== ===============================================================================================================
140	:meth:`G2Phase.set_refinements` Provides a mechanism to set values and refinement flags for the phase. See :ref:`Phase_parameters_table`
141	for more details. This information also can be supplied within a call to :meth:`G2Project.do_refinements`
142	or :meth:`G2Project.set_refinement`.
143	:meth:`G2Phase.clear_refinements` Unsets refinement flags for the phase.
144	:meth:`G2Phase.set_HAP_refinements` Provides a mechanism to set values and refinement flags for parameters specific to both this phase and
145	one of its histograms. See :ref:`HAP_parameters_table`. This information also can be supplied within
146	a call to :meth:`G2Project.do_refinements` or :meth:`G2Project.set_refinement`.
147	:meth:`G2Phase.clear_HAP_refinements` Clears refinement flags specific to both this phase and one of its histograms.
148	:meth:`G2Phase.getHAPvalues` Returns values of parameters specific to both this phase and one of its histograms.
149	:meth:`G2Phase.copyHAPvalues` Copies HAP settings between from one phase/histogram and to other histograms in same phase.
150	:meth:`G2Phase.atoms` Returns a list of atoms in the phase
151	:meth:`G2Phase.atom` Returns an atom from its label
152	:meth:`G2Phase.histograms` Returns a list of histograms linked to the phase
153	:meth:`G2Phase.get_cell` Returns unit cell parameters (also see :meth:`G2Phase.get_cell_and_esd`)
154	:meth:`G2Phase.export_CIF` Writes a CIF for the phase
155	:meth:`G2Phase.set_Controls` Set overall GSAS-II control settings such as number of cycles and to set up a sequential
156	fit. (Also see :meth:`G2Phase.get_Controls` to read values.)
157	================================================== ===============================================================================================================
158
159	---------------------
160	:class:`G2PwdrData`
161	---------------------
162
163	Another common object in GSASIIscriptable scripts is :class:`G2PwdrData`, which encapsulate each powder diffraction histogram in a project, with commonly used methods:
164
165	.. tabularcolumns:: \|l\|p{3.5in}\|
166
167	================================================== ===============================================================================================================
168	method Use
169	================================================== ===============================================================================================================
170	:meth:`G2PwdrData.set_refinements` Provides a mechanism to set values and refinement flags for the powder histogram. See
171	:ref:`Histogram_parameters_table` for details.
172	:meth:`G2PwdrData.clear_refinements` Unsets refinement flags for the the powder histogram.
173	:meth:`G2PwdrData.residuals` Reports R-factors etc. for the the powder histogram (also see :meth:`G2PwdrData.get_wR`)
174	:meth:`G2PwdrData.add_back_peak` Adds a background peak to the histogram. Also see :meth:`G2PwdrData.del_back_peak` and
175	:meth:`G2PwdrData.ref_back_peak`.
176	:meth:`G2PwdrData.fit_fixed_points` Fits background to the specified fixed points.
177	:meth:`G2PwdrData.getdata` Provides access to the diffraction data associated with the histogram.
178	:meth:`G2PwdrData.Export` Writes the diffraction data into a file
179	================================================== ===============================================================================================================
180
181	---------------------
182	:class:`G2Image`
183	---------------------
184
185	When working with images, there will be a :class:`G2Image` object for each image (also see :meth:`G2Project.add_image` and :meth:`G2Project.images`).
186
187	.. tabularcolumns:: \|l\|p{3.5in}\|
188
189	================================================== ===============================================================================================================
190	method Use
191	================================================== ===============================================================================================================
192	:meth:`G2Image.Recalibrate` Invokes a recalibration fit starting from the current Image Controls calibration coefficients.
193	:meth:`G2Image.Integrate` Invokes an image integration All parameters Image Controls will have previously been set.
194	:meth:`G2Image.setControl` Set an Image Controls parameter in the current image.
195	:meth:`G2Image.getControl` Return an Image Controls parameter in the current image.
196	:meth:`G2Image.findControl` Get the names of Image Controls parameters.
197	:meth:`G2Image.loadControls` Load controls from a .imctrl file (also see :meth:`G2Image.saveControls`).
198	:meth:`G2Image.loadMasks` Load masks from a .immask file.
199	:meth:`G2Image.setVary` Set a refinement flag for Image Controls parameter in the current image. (Also see :meth:`G2Image.getVary`)
200	:meth:`G2Image.setCalibrant` Set a calibrant type (or show choices) for the current image.
201	:meth:`G2Image.setControlFile` Set a image to be used as a background/dark/gain map image.
202	================================================== ===============================================================================================================
203
204	----------------------
205	:class:`G2AtomRecord`
206	----------------------
207
208	When working with phases, :class:`G2AtomRecord` objects provide access to the contents of each atom in a phase. This provides access to "properties" that can be
209	used to get values of much of the atoms associated settings: label, type, refinement_flags, coordinates, occupancy, ranId, adp_flag, and uiso. In addition,
210	refinement_flags, occupancy and uiso can be used to set values. See the :class:`G2AtomRecord` docs and source code.
211
212	.. _Refinement_dicts:
213
214	=====================
215	Refinement parameters
216	=====================
217	While scripts can be written that setup refinements by changing individual parameters
218	through calls to the methods associated with objects that wrap each data tree item,
219	many of these actions can be combined into fairly complex dict structures to conduct refinement
220	steps. Use of these dicts is required with the :ref:`CommandlineInterface`. This section of the
221	documentation describes these dicts.
222
223	.. _Project_dicts:
224
225	-----------------------------
226	Project-level Parameter Dict
227	-----------------------------
228
229	As noted below (:ref:`Refinement_parameters_kinds`), there are three types of refinement parameters,
230	which can be accessed individually by the objects that encapsulate individual phases and histograms
231	but it will often be simplest to create a composite dictionary
232	that is used at the project-level. A dict is created with keys
233	"set" and "clear" that can be supplied to :meth:`G2Project.set_refinement`
234	(or :meth:`G2Project.do_refinements`, see :ref:`Refinement_recipe` below) that will
235	determine parameter values and will determine which parameters will be refined.
236
237	The specific keys and subkeys that can be used are defined in tables
238	:ref:`Histogram_parameters_table`, :ref:`Phase_parameters_table` and :ref:`HAP_parameters_table`.
239
240	Note that optionally a list of histograms and/or phases can be supplied in the call to
241	:meth:`G2Project.set_refinement`, but if not specified, the default is to use all defined
242	phases and histograms.
243
244	As an example:
245
246	.. code-block:: python
247
248	pardict = {'set': { 'Limits': [0.8, 12.0],
249	'Sample Parameters': ['Absorption', 'Contrast', 'DisplaceX'],
250	'Background': {'type': 'chebyschev', 'refine': True,
251	'peaks':[[0,True],[1,1,1]] }},
252	'clear': {'Instrument Parameters': ['U', 'V', 'W']}}
253	my_project.set_refinement(pardict)
254
255	.. _Refinement_recipe:
256
257	------------------------
258	Refinement recipe
259	------------------------
260	Building on the :ref:`Project_dicts`,
261	it is possible to specify a sequence of refinement actions as a list of
262	these dicts and supplying this list
263	as an argument to :meth:`G2Project.do_refinements`.
264
265	As an example, this code performs the same actions as in the example in the section above:
266
267	.. code-block:: python
268
269	pardict = {'set': { 'Limits': [0.8, 12.0],
270	'Sample Parameters': ['Absorption', 'Contrast', 'DisplaceX'],
271	'Background': {'type': 'chebyschev', 'refine': True}},
272	'clear': {'Instrument Parameters': ['U', 'V', 'W']}}
273	my_project.do_refinements([pardict])
274
275	However, in addition to setting a number of parameters, this example will perform a refinement as well,
276	after setting the parameters. More than one refinement can be performed by including more
277	than one dict in the list.
278
279	In this example, two refinement steps will be performed:
280
281	.. code-block:: python
282
283	my_project.do_refinements([pardict,pardict1])
284
285
286	The keys defined in the following table
287	may be used in a dict supplied to :meth:`G2Project.do_refinements`. Note that keys ``histograms``
288	and ``phases`` are used to limit actions to specific sets of parameters within the project.
289
290	========== ============================================================================
291	key explanation
292	========== ============================================================================
293	set Specifies a dict with keys and subkeys as described in the
294	:ref:`Refinement_parameters_fmt` section. Items listed here
295	will be set to be refined.
296	clear Specifies a dict, as above for set, except that parameters are
297	cleared and thus will not be refined.
298	once Specifies a dict as above for set, except that parameters are
299	set for the next cycle of refinement and are cleared once the
300	refinement step is completed.
301	skip Normally, once parameters are processed with a set/clear/once
302	action(s), a refinement is started. If skip is defined as True
303	(or any other value) the refinement step is not performed.
304	output If a file name is specified for output is will be used to save
305	the current refinement.
306	histograms Should contain a list of histogram(s) to be used for the
307	set/clear/once action(s) on :ref:`Histogram_parameters_table` or
308	:ref:`HAP_parameters_table`. Note that this will be
309	ignored for :ref:`Phase_parameters_table`. Histograms may be
310	specified as a list of strings [('PWDR ...'),...], indices
311	[0,1,2] or as list of objects [hist1, hist2].
312	phases Should contain a list of phase(s) to be used for the
313	set/clear/once action(s) on :ref:`Phase_parameters_table` or
314	:ref:`HAP_parameters_table`. Note that this will be
315	ignored for :ref:`Histogram_parameters_table`.
316	Phases may be specified as a list of strings
317	[('Phase name'),...], indices [0,1,2] or as list of objects
318	[phase0, phase2].
319	call Specifies a function to call after a refinement is completed.
320	The value supplied can be the object (typically a function)
321	that will be called or a string that will evaluate (in the
322	namespace inside :meth:`G2Project.iter_refinements` where
323	``self`` references the project.)
324	Nothing is called if this is not specified.
325	callargs Provides a list of arguments that will be passed to the function
326	in call (if any). If call is defined and callargs is not, the
327	current <tt>G2Project</tt> is passed as a single argument.
328	========== ============================================================================
329
330	An example that performs a series of refinement steps follows:
331
332	.. code-block:: python
333
334	reflist = [
335	{"set": { "Limits": { "low": 0.7 },
336	"Background": { "no. coeffs": 3,
337	"refine": True }}},
338	{"set": { "LeBail": True,
339	"Cell": True }},
340	{"set": { "Sample Parameters": ["DisplaceX"]}},
341	{"set": { "Instrument Parameters": ["U", "V", "W", "X", "Y"]}},
342	{"set": { "Mustrain": { "type": "uniaxial",
343	"refine": "equatorial",
344	"direction": [0, 0, 1]}}},
345	{"set": { "Mustrain": { "type": "uniaxial",
346	"refine": "axial"}}},
347	{"clear": { "LeBail": True},
348	"set": { "Atoms": { "Mn": "X" }}},
349	{"set": { "Atoms": { "O1": "X", "O2": "X" }}},]
350	my_project.do_refinements(reflist)
351
352
353	In this example, a separate refinement step will be performed for each dict in the list. The keyword
354	"skip" can be used to specify a dict that should not include a refinement.
355	Note that in the second from last refinement step, parameters are both set and cleared.
356
357	.. _Refinement_parameters_kinds:
358
359	----------------------------
360	Refinement parameter types
361	----------------------------
362
363	Note that parameters and refinement flags used in GSAS-II fall into three classes:
364
365	* Histogram: There will be a set of these for each dataset loaded into a
366	project file. The parameters available depend on the type of histogram
367	(Bragg-Brentano, Single-Crystal, TOF,...). Typical Histogram parameters
368	include the overall scale factor, background, instrument and sample parameters;
369	see the :ref:`Histogram_parameters_table` table for a list of the histogram
370	parameters where access has been provided.
371
372	* Phase: There will be a set of these for each phase loaded into a
373	project file. While some parameters are found in all types of phases,
374	others are only found in certain types (modulated, magnetic, protein...).
375	Typical phase parameters include unit cell lengths and atomic positions; see the
376	:ref:`Phase_parameters_table` table for a list of the phase
377	parameters where access has been provided.
378
379	* Histogram-and-phase (HAP): There is a set of these for every histogram
380	that is associated with each phase, so that if there are ``N`` phases and ``M``
381	histograms, there can be ``N*M`` total sets of "HAP" parameters sets (fewer if all
382	histograms are not linked to all phases.) Typical HAP parameters include the
383	phase fractions, sample microstrain and crystallite size broadening terms,
384	hydrostatic strain perturbations of the unit cell and preferred orientation
385	values.
386	See the :ref:`HAP_parameters_table` table for the HAP parameters where access has
387	been provided.
388
389	.. _Refinement_parameters_fmt:
390
391	=================================
392	Specifying Refinement Parameters
393	=================================
394
395	Refinement parameter values and flags to turn refinement on and off are specified within dictionaries,
396	where the details of these dicts are organized depends on the
397	type of parameter (see :ref:`Refinement_parameters_kinds`), with a different set
398	of keys (as described below) for each of the three types of parameters.
399
400	.. _Histogram_parameters_table:
401
402	--------------------
403	Histogram parameters
404	--------------------
405
406	This table describes the dictionaries supplied to :func:`G2PwdrData.set_refinements`
407	and :func:`G2PwdrData.clear_refinements`. As an example,
408
409	.. code-block:: python
410
411	hist.set_refinements({"Background": {"no.coeffs": 3, "refine": True},
412	"Sample Parameters": ["Scale"],
413	"Limits": [10000, 40000]})
414
415	With :meth:`G2Project.do_refinements`, these parameters should be placed inside a dict with a key
416	``set``, ``clear``, or ``once``. Values will be set for all histograms, unless the ``histograms``
417	key is used to define specific histograms. As an example:
418
419	.. code-block:: python
420
421	gsas_proj.do_refinements([
422	{'set': {
423	'Background': {'no.coeffs': 3, 'refine': True},
424	'Sample Parameters': ['Scale'],
425	'Limits': [10000, 40000]},
426	'histograms': [1,2]}
427	])
428
429	Note that below in the Instrument Parameters section,
430	related profile parameters (such as U and V) are grouped together but
431	separated by commas to save space in the table.
432
433	.. tabularcolumns:: \|l\|l\|p{3.5in}\|
434
435	===================== ==================== =================================================
436	key subkey explanation
437	===================== ==================== =================================================
438	Limits The range of 2-theta (degrees) or TOF (in
439	microsec) range of values to use. Can
440	be either a dictionary of 'low' and/or 'high',
441	or a list of 2 items [low, high]
442	\ low Sets the low limit
443	\ high Sets the high limit
444
445	Sample Parameters Should be provided as a list of subkeys
446	to set or clear, e.g. ['DisplaceX', 'Scale']
447	\ Absorption
448	\ Contrast
449	\ DisplaceX Sample displacement along the X direction
450	\ DisplaceY Sample displacement along the Y direction
451	\ Scale Histogram Scale factor
452
453	Background Sample background. Value will be a dict or
454	a boolean. If True or False, the refine
455	parameter for background is set to that.
456	Note that background peaks are not handled
457	via this; see
458	:meth:`G2PwdrData.ref_back_peak` instead.
459	When value is a dict,
460	supply any of the following keys:
461	\ type The background model, e.g. 'chebyschev'
462	\ refine The value of the refine flag, boolean
463	\ no. coeffs Number of coefficients to use, integer
464	\ coeffs List of floats, literal values for background
465	\ FixedPoints List of (2-theta, intensity) values for fixed points
466	\ fit fixed points If True, triggers a fit to the fixed points to
467	be calculated. It is calculated when this key is
468	detected, regardless of calls to refine.
469	peaks Specifies a set of flags for refining
470	background peaks as a nested list. There may
471	be an item for each defined background peak
472	(or fewer) and each item is a list with the flag
473	values for pos,int,sig & gam (fewer than 4 values
474	are allowed).
475
476	Instrument Parameters As in Sample Paramters, provide as a list of
477	subkeys to
478	set or clear, e.g. ['X', 'Y', 'Zero', 'SH/L']
479	\ U, V, W Gaussian peak profile terms
480	\ X, Y, Z Lorentzian peak profile terms
481	\ alpha, beta-0, TOF profile terms
482	beta-1, beta-q,
483	\ sig-0, sig-1, TOF profile terms
484	sig-2, sig-q
485	\ difA, difB, difC TOF Calibration constants
486	\ Zero Zero shift
487	\ SH/L Finger-Cox-Jephcoat low-angle peak asymmetry
488	\ Polariz. Polarization parameter
489	\ Lam Lambda, the incident wavelength
490	===================== ==================== =================================================
491
492	.. _Phase_parameters_table:
493
494	----------------
495	Phase parameters
496	----------------
497
498	This table describes the dictionaries supplied to :func:`G2Phase.set_refinements`
499	and :func:`G2Phase.clear_refinements`. With :meth:`G2Project.do_refinements`,
500	these parameters should be placed inside a dict with a key
501	``set``, ``clear``, or ``once``. Values will be set for all phases, unless the ``phases``
502	key is used to define specific phase(s).
503
504
505	.. tabularcolumns:: \|l\|p{4.5in}\|
506
507	======= ==========================================================
508	key explanation
509	======= ==========================================================
510	Cell Whether or not to refine the unit cell.
511	Atoms Dictionary of atoms and refinement flags.
512	Each key should be an atom label, e.g.
513	'O3', 'Mn5', and each value should be
514	a string defining what values to refine.
515	Values can be any combination of 'F'
516	for fractional occupancy, 'X' for position,
517	and 'U' for Debye-Waller factor
518	LeBail Enables LeBail intensity extraction.
519	======= ==========================================================
520
521
522	.. _HAP_parameters_table:
523
524
525	Histogram-and-phase parameters
526	------------------------------
527
528	This table describes the dictionaries supplied to :func:`G2Phase.set_HAP_refinements`
529	and :func:`G2Phase.clear_HAP_refinements`. When supplied to
530	:meth:`G2Project.do_refinements`, these parameters should be placed inside a dict with a key
531	``set``, ``clear``, or ``once``. Values will be set for all histograms used in each phase,
532	unless the ``histograms`` and ``phases`` keys are used to define specific phases and histograms.
533
534	.. tabularcolumns:: \|l\|l\|p{3.5in}\|
535
536	============= ========== ============================================================
537	key subkey explanation
538	============= ========== ============================================================
539	Babinet Should be a list of the following
540	subkeys. If not, assumes both
541	BabA and BabU
542	\ BabA
543	\ BabU
544	Extinction Boolean, True to refine.
545	HStrain Boolean or list/tuple, True to refine all
546	appropriate D\ :sub:`ij` terms or False
547	to not refine any. If a list/tuple, will
548	be a set of True & False values for each
549	D\ :sub:`ij` term; number of items must
550	match number of terms.
551	Mustrain
552	\ type Mustrain model. One of 'isotropic',
553	'uniaxial', or 'generalized'. **Should always
554	be included when Mustrain is used.**
555	\ direction For uniaxial only. A list of three
556	integers,
557	the [hkl] direction of the axis.
558	\ refine Usually boolean, set to True to refine.
559	or False to clear.
560	For uniaxial model, can specify a value
561	of 'axial' or 'equatorial' to set that flag
562	to True or a single
563	boolean sets both axial and equatorial.
564	Size
565	\ type Size broadening model. One of 'isotropic',
566	'uniaxial', or 'ellipsoid'. **Should always
567	be specified when Size is used.**
568	\ direction For uniaxial only. A list of three
569	integers,
570	the [hkl] direction of the axis.
571	\ refine Boolean, True to refine.
572	\ value float, size value in microns
573	Pref.Ori. Boolean, True to refine
574	Show Boolean, True to refine
575	Use Boolean, True to refine
576	Scale Phase fraction; Boolean, True to refine
577	============= ========== ============================================================
578
579	------------------------
580	Histogram/Phase objects
581	------------------------
582	Each phase and powder histogram in a :class:`G2Project` object has an associated
583	object. Parameters within each individual object can be turned on and off by calling
584	:meth:`G2PwdrData.set_refinements` or :meth:`G2PwdrData.clear_refinements`
585	for histogram parameters;
586	:meth:`G2Phase.set_refinements` or :meth:`G2Phase.clear_refinements`
587	for phase parameters; and :meth:`G2Phase.set_HAP_refinements` or
588	:meth:`G2Phase.clear_HAP_refinements`. As an example, if some_histogram is a histogram object (of type :class:`G2PwdrData`), use this to set parameters in that histogram:
589
590	.. code-block:: python
591
592	params = { 'Limits': [0.8, 12.0],
593	'Sample Parameters': ['Absorption', 'Contrast', 'DisplaceX'],
594	'Background': {'type': 'chebyschev', 'refine': True}}
595	some_histogram.set_refinements(params)
596
597	Likewise to turn refinement flags on, use code such as this:
598
599	.. code-block:: python
600
601	params = { 'Instrument Parameters': ['U', 'V', 'W']}
602	some_histogram.set_refinements(params)
603
604	and to turn these refinement flags, off use this (Note that the
605	``.clear_refinements()`` methods will usually will turn off refinement even
606	if a refinement parameter is set in the dict to True.):
607
608	.. code-block:: python
609
610	params = { 'Instrument Parameters': ['U', 'V', 'W']}
611	some_histogram.clear_refinements(params)
612
613	For phase parameters, use code such as this:
614
615	.. code-block:: python
616
617	params = { 'LeBail': True, 'Cell': True,
618	'Atoms': { 'Mn1': 'X',
619	'O3': 'XU',
620	'V4': 'FXU'}}
621	some_histogram.set_refinements(params)
622
623
624	and here is an example for HAP parameters:
625
626	.. code-block:: python
627
628	params = { 'Babinet': 'BabA',
629	'Extinction': True,
630	'Mustrain': { 'type': 'uniaxial',
631	'direction': [0, 0, 1],
632	'refine': True}}
633	some_phase.set_HAP_refinements(params)
634
635	Note that the parameters must match the object type and method (phase vs. histogram vs. HAP).
636
637	.. _CommandlineInterface:
638
639	=======================================
640	GSASIIscriptable Command-line Interface
641	=======================================
642
643	The routines described above are intended to be called from a Python script, but an
644	alternate way to access some of the same functionality is to
645	invoke the ``GSASIIscriptable.py`` script from
646	the command line usually from within a shell script or batch file. This
647	will usually be done with a command such as::
648
649	python <path/>GSASIIscriptable.py <subcommand> <file.gpx> <options>
650
651	The following subcommands are defined:
652
653	* create, see :func:`create`
654	* add, see :func:`add`
655	* dump, see :func:`dump`
656	* refine, see :func:`refine`
657	* export, :func:`export`
658	* browse, see :func:`IPyBrowse`
659
660	Run::
661
662	python GSASIIscriptable.py --help
663
664	to show the available subcommands, and inspect each subcommand with
665	`python GSASIIscriptable.py <subcommand> --help` or see the documentation for each of the above routines.
666
667	.. _JsonFormat:
668
669	-------------------------
670	Parameters in JSON files
671	-------------------------
672
673	The refine command requires two inputs: an existing GSAS-II project (.gpx) file and
674	a JSON format file
675	(see `Introducing JSON <http://json.org/>`_) that contains a single dict.
676	This dict may have two keys:
677
678	refinements:
679	This defines the a set of refinement steps in a JSON representation of a
680	:ref:`Refinement_recipe` list.
681
682	code:
683	This optionally defines Python code that will be executed after the project is loaded,
684	but before the refinement is started. This can be used to execute Python code to change
685	parameters that are not accessible via a :ref:`Refinement_recipe` dict (note that the
686	project object is accessed with variable ``proj``) or to define code that will be called
687	later (see key ``call`` in the :ref:`Refinement_recipe` section.)
688
689	JSON website: `Introducing JSON <http://json.org/>`_.
690
691	.. _API:
692
693	============================================================
694	API: Complete Documentation
695	============================================================
696
697	The large number of classes and modules in this module are described below.
698	A script will have one or more G2Project objects using :class:`G2Project` and then
699	perform actions such as adding a histogram (method :meth:`G2Project.add_powder_histogram`),
700	adding a phase (method :meth:`G2Project.add_phase`),
701	or setting parameters and performing a refinement
702	(method :meth:`G2Project.do_refinements`).
703
704	To change settings within histograms, images and phases, one usually needs to use
705	methods inside :class:`G2PwdrData`, :class:`G2Image` or :class:`G2Phase`.
706
707	"""
708	from __future__ import division, print_function
709	import argparse
710	import os.path as ospath
711	import datetime as dt
712	import sys
713	import platform
714	if '2' in platform.python_version_tuple()[0]:
715	import cPickle
716	strtypes = (str,unicode)
717	else:
718	import pickle as cPickle
719	strtypes = (str,bytes)
720	import imp
721	import copy
722	import os
723	import random as ran
724
725	import numpy.ma as ma
726	import scipy.interpolate as si
727	import numpy as np
728	import scipy as sp
729
730	import GSASIIpath
731	GSASIIpath.SetBinaryPath(True) # for now, this is needed before some of these modules can be imported
732	import GSASIIobj as G2obj
733	import GSASIIpwd as G2pwd
734	import GSASIIstrMain as G2strMain
735	#import GSASIIIO as G2IO
736	import GSASIIstrIO as G2strIO
737	import GSASIIspc as G2spc
738	import GSASIIElem as G2elem
739	import GSASIIfiles as G2fil
740	import GSASIIimage as G2img
741
742	# Delay imports to not slow down small scripts that don't need them
743	Readers = {'Pwdr':[], 'Phase':[], 'Image':[]}
744	'''Readers by reader type'''
745	exportersByExtension = {}
746	'''Specifies the list of extensions that are supported for Powder data export'''
747	npsind = lambda x: np.sin(x*np.pi/180.)
748
749	def LoadG2fil():
750	"""Setup GSAS-II importers. Delay importing this module, it is slow"""
751	if len(Readers['Pwdr']) > 0: return
752	# initialize imports
753	Readers['Pwdr'] = G2fil.LoadImportRoutines("pwd", "Powder_Data")
754	Readers['Phase'] = G2fil.LoadImportRoutines("phase", "Phase")
755	Readers['Image'] = G2fil.LoadImportRoutines("img", "Image")
756
757	# initialize exports
758	for obj in exportersByExtension:
759	try:
760	obj.Writer
761	except AttributeError:
762	continue
763	for typ in obj.exporttype:
764	if typ not in exportersByExtension:
765	exportersByExtension[typ] = {obj.extension:obj}
766	else:
767	exportersByExtension[typ][obj.extension] = obj
768
769	def LoadDictFromProjFile(ProjFile):
770	'''Read a GSAS-II project file and load items to dictionary
771
772	:param str ProjFile: GSAS-II project (name.gpx) full file name
773	:returns: Project,nameList, where
774
775	* Project (dict) is a representation of gpx file following the GSAS-II tree structure
776	for each item: key = tree name (e.g. 'Controls','Restraints',etc.), data is dict
777	data dict = {'data':item data whch may be list, dict or None,'subitems':subdata (if any)}
778	* nameList (list) has names of main tree entries & subentries used to reconstruct project file
779
780	Example for fap.gpx::
781
782	Project = { #NB:dict order is not tree order
783	'Phases':{'data':None,'fap':{phase dict}},
784	'PWDR FAP.XRA Bank 1':{'data':[histogram data list],'Comments':comments,'Limits':limits, etc},
785	'Rigid bodies':{'data': {rigid body dict}},
786	'Covariance':{'data':{covariance data dict}},
787	'Controls':{'data':{controls data dict}},
788	'Notebook':{'data':[notebook list]},
789	'Restraints':{'data':{restraint data dict}},
790	'Constraints':{'data':{constraint data dict}}]
791	}
792	nameList = [ #NB: reproduces tree order
793	['Notebook',],
794	['Controls',],
795	['Covariance',],
796	['Constraints',],
797	['Restraints',],
798	['Rigid bodies',],
799	['PWDR FAP.XRA Bank 1',
800	'Comments',
801	'Limits',
802	'Background',
803	'Instrument Parameters',
804	'Sample Parameters',
805	'Peak List',
806	'Index Peak List',
807	'Unit Cells List',
808	'Reflection Lists'],
809	['Phases', 'fap']
810	]
811	'''
812	# Let IOError be thrown if file does not exist
813	if not ospath.exists(ProjFile):
814	print ('\n*** Error attempt to open project file that does not exist: \n {}'.
815	format(ProjFile))
816	raise IOError('GPX file {} does not exist'.format(ProjFile))
817	try:
818	Project, nameList = G2strIO.GetFullGPX(ProjFile)
819	except Exception as msg:
820	raise IOError(msg)
821	return Project,nameList
822
823	def SaveDictToProjFile(Project,nameList,ProjFile):
824	'''Save a GSAS-II project file from dictionary/nameList created by LoadDictFromProjFile
825
826	:param dict Project: representation of gpx file following the GSAS-II
827	tree structure as described for LoadDictFromProjFile
828	:param list nameList: names of main tree entries & subentries used to reconstruct project file
829	:param str ProjFile: full file name for output project.gpx file (including extension)
830	'''
831	file = open(ProjFile,'wb')
832	try:
833	for name in nameList:
834	data = []
835	item = Project[name[0]]
836	data.append([name[0],item['data']])
837	for item2 in name[1:]:
838	data.append([item2,item[item2]])
839	cPickle.dump(data,file,1)
840	finally:
841	file.close()
842	print('gpx file saved as %s'%ProjFile)
843
844	# def ImportPowder(reader,filename):
845	# '''Use a reader to import a powder diffraction data file
846
847	# :param str reader: a scriptable reader
848	# :param str filename: full name of powder data file; can be "multi-Bank" data
849
850	# :returns: list rdlist: list of reader objects containing powder data, one for each
851	# "Bank" of data encountered in file. Items in reader object of interest are:
852
853	# * rd.comments: list of str: comments found on powder file
854	# * rd.dnames: list of str: data nammes suitable for use in GSASII data tree NB: duplicated in all rd entries in rdlist
855	# * rd.powderdata: list of numpy arrays: pos,int,wt,zeros,zeros,zeros as needed for a PWDR entry in GSASII data tree.
856	# '''
857	# rdfile,rdpath,descr = imp.find_module(reader)
858	# rdclass = imp.load_module(reader,rdfile,rdpath,descr)
859	# rd = rdclass.GSAS_ReaderClass()
860	# if not rd.scriptable:
861	# print(u'**** ERROR: '+reader+u' is not a scriptable reader')
862	# return None
863	# rdlist = []
864	# if rd.ContentsValidator(filename):
865	# repeat = True
866	# rdbuffer = {} # create temporary storage for file reader
867	# block = 0
868	# while repeat: # loop if the reader asks for another pass on the file
869	# block += 1
870	# repeat = False
871	# rd.objname = ospath.basename(filename)
872	# flag = rd.Reader(filename,None,buffer=rdbuffer,blocknum=block,)
873	# if flag:
874	# rdlist.append(copy.deepcopy(rd)) # save the result before it is written over
875	# if rd.repeat:
876	# repeat = True
877	# return rdlist
878	# print(rd.errors)
879	# return None
880
881	def SetDefaultDData(dType,histoName,NShkl=0,NDij=0):
882	'''Create an initial Histogram dictionary
883
884	Author: Jackson O'Donnell (jacksonhodonnell .at. gmail.com)
885	'''
886	if dType in ['SXC','SNC']:
887	return {'Histogram':histoName,'Show':False,'Scale':[1.0,True],
888	'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},
889	'Extinction':['Lorentzian','None', {'Tbar':0.1,'Cos2TM':0.955,
890	'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]}],
891	'Flack':[0.0,False]}
892	elif dType == 'SNT':
893	return {'Histogram':histoName,'Show':False,'Scale':[1.0,True],
894	'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},
895	'Extinction':['Lorentzian','None', {
896	'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]}]}
897	elif 'P' in dType:
898	return {'Histogram':histoName,'Show':False,'Scale':[1.0,False],
899	'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{},[],0.1],
900	'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1],
901	[1.,1.,1.,0.,0.,0.],6*[False,]],
902	'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1],
903	NShkl[0.01,],NShkl[False,]],
904	'HStrain':[NDij[0.0,],NDij[False,]],
905	'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}}
906
907
908	def PreSetup(data):
909	'''Create part of an initial (empty) phase dictionary
910
911	from GSASIIphsGUI.py, near end of UpdatePhaseData
912
913	Author: Jackson O'Donnell (jacksonhodonnell .at. gmail.com)
914	'''
915	if 'RBModels' not in data:
916	data['RBModels'] = {}
917	if 'MCSA' not in data:
918	data['MCSA'] = {'Models':[{'Type':'MD','Coef':[1.0,False,[.8,1.2],],'axis':[0,0,1]}],'Results':[],'AtInfo':{}}
919	if 'dict' in str(type(data['MCSA']['Results'])):
920	data['MCSA']['Results'] = []
921	if 'Modulated' not in data['General']:
922	data['General']['Modulated'] = False
923	# if 'modulated' in data['General']['Type']:
924	# data['General']['Modulated'] = True
925	# data['General']['Type'] = 'nuclear'
926
927
928	def SetupGeneral(data, dirname):
929	"""Helps initialize phase data.
930
931	From GSASIIphsGui.py, function of the same name. Minor changes for imports etc.
932
933	Author: Jackson O'Donnell (jacksonhodonnell .at. gmail.com)
934	"""
935	mapDefault = {'MapType':'','RefList':'','Resolution':0.5,'Show bonds':True,
936	'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
937	generalData = data['General']
938	atomData = data['Atoms']
939	generalData['AtomTypes'] = []
940	generalData['Isotopes'] = {}
941
942	if 'Isotope' not in generalData:
943	generalData['Isotope'] = {}
944	if 'Data plot type' not in generalData:
945	generalData['Data plot type'] = 'Mustrain'
946	if 'POhkl' not in generalData:
947	generalData['POhkl'] = [0,0,1]
948	if 'Map' not in generalData:
949	generalData['Map'] = mapDefault.copy()
950	if 'Flip' not in generalData:
951	generalData['Flip'] = {'RefList':'','Resolution':0.5,'Norm element':'None',
952	'k-factor':0.1,'k-Max':20.,}
953	if 'testHKL' not in generalData['Flip']:
954	generalData['Flip']['testHKL'] = [[0,0,2],[2,0,0],[1,1,1],[0,2,0],[1,2,3]]
955	if 'doPawley' not in generalData:
956	generalData['doPawley'] = False #ToDo: change to ''
957	if 'Pawley dmin' not in generalData:
958	generalData['Pawley dmin'] = 1.0
959	if 'Pawley neg wt' not in generalData:
960	generalData['Pawley neg wt'] = 0.0
961	if 'Algolrithm' in generalData.get('MCSA controls',{}) or \
962	'MCSA controls' not in generalData:
963	generalData['MCSA controls'] = {'Data source':'','Annealing':[50.,0.001,50],
964	'dmin':2.0,'Algorithm':'log','Jump coeff':[0.95,0.5],'boltzmann':1.0,
965	'fast parms':[1.0,1.0,1.0],'log slope':0.9,'Cycles':1,'Results':[],'newDmin':True}
966	if 'AtomPtrs' not in generalData:
967	generalData['AtomPtrs'] = [3,1,7,9]
968	if generalData['Type'] == 'macromolecular':
969	generalData['AtomPtrs'] = [6,4,10,12]
970	elif generalData['Type'] == 'magnetic':
971	generalData['AtomPtrs'] = [3,1,10,12]
972	if generalData['Modulated']:
973	generalData['Type'] = 'nuclear'
974	if 'Super' not in generalData:
975	generalData['Super'] = 1
976	generalData['SuperVec'] = [[0,0,.1],False,4]
977	generalData['SSGData'] = {}
978	if '4DmapData' not in generalData:
979	generalData['4DmapData'] = mapDefault.copy()
980	generalData['4DmapData'].update({'MapType':'Fobs'})
981	if 'Modulated' not in generalData:
982	generalData['Modulated'] = False
983	if 'HydIds' not in generalData:
984	generalData['HydIds'] = {}
985	cx,ct,cs,cia = generalData['AtomPtrs']
986	generalData['NoAtoms'] = {}
987	generalData['BondRadii'] = []
988	generalData['AngleRadii'] = []
989	generalData['vdWRadii'] = []
990	generalData['AtomMass'] = []
991	generalData['Color'] = []
992	if generalData['Type'] == 'magnetic':
993	generalData['MagDmin'] = generalData.get('MagDmin',1.0)
994	landeg = generalData.get('Lande g',[])
995	generalData['Mydir'] = dirname
996	badList = {}
997	for iat,atom in enumerate(atomData):
998	atom[ct] = atom[ct].lower().capitalize() #force to standard form
999	if generalData['AtomTypes'].count(atom[ct]):
1000	generalData['NoAtoms'][atom[ct]] += atom[cx+3]*float(atom[cs+1])
1001	elif atom[ct] != 'UNK':
1002	Info = G2elem.GetAtomInfo(atom[ct])
1003	if not Info:
1004	if atom[ct] not in badList:
1005	badList[atom[ct]] = 0
1006	badList[atom[ct]] += 1
1007	atom[ct] = 'UNK'
1008	continue
1009	atom[ct] = Info['Symbol'] # N.B. symbol might be changed by GetAtomInfo
1010	generalData['AtomTypes'].append(atom[ct])
1011	generalData['Z'] = Info['Z']
1012	generalData['Isotopes'][atom[ct]] = Info['Isotopes']
1013	generalData['BondRadii'].append(Info['Drad'])
1014	generalData['AngleRadii'].append(Info['Arad'])
1015	generalData['vdWRadii'].append(Info['Vdrad'])
1016	if atom[ct] in generalData['Isotope']:
1017	if generalData['Isotope'][atom[ct]] not in generalData['Isotopes'][atom[ct]]:
1018	isotope = list(generalData['Isotopes'][atom[ct]].keys())[-1]
1019	generalData['Isotope'][atom[ct]] = isotope
1020	generalData['AtomMass'].append(Info['Isotopes'][generalData['Isotope'][atom[ct]]]['Mass'])
1021	else:
1022	generalData['Isotope'][atom[ct]] = 'Nat. Abund.'
1023	if 'Nat. Abund.' not in generalData['Isotopes'][atom[ct]]:
1024	isotope = list(generalData['Isotopes'][atom[ct]].keys())[-1]
1025	generalData['Isotope'][atom[ct]] = isotope
1026	generalData['AtomMass'].append(Info['Mass'])
1027	generalData['NoAtoms'][atom[ct]] = atom[cx+3]*float(atom[cs+1])
1028	generalData['Color'].append(Info['Color'])
1029	if generalData['Type'] == 'magnetic':
1030	if len(landeg) < len(generalData['AtomTypes']):
1031	landeg.append(2.0)
1032	if generalData['Type'] == 'magnetic':
1033	generalData['Lande g'] = landeg[:len(generalData['AtomTypes'])]
1034
1035	if badList:
1036	msg = 'Warning: element symbol(s) not found:'
1037	for key in badList:
1038	msg += '\n\t' + key
1039	if badList[key] > 1:
1040	msg += ' (' + str(badList[key]) + ' times)'
1041	raise G2ScriptException("Phase error:\n" + msg)
1042	# wx.MessageBox(msg,caption='Element symbol error')
1043	F000X = 0.
1044	F000N = 0.
1045	for i,elem in enumerate(generalData['AtomTypes']):
1046	F000X += generalData['NoAtoms'][elem]*generalData['Z']
1047	isotope = generalData['Isotope'][elem]
1048	F000N += generalData['NoAtoms'][elem]*generalData['Isotopes'][elem][isotope]['SL'][0]
1049	generalData['F000X'] = F000X
1050	generalData['F000N'] = F000N
1051	import GSASIImath as G2mth
1052	generalData['Mass'] = G2mth.getMass(generalData)
1053
1054
1055	def make_empty_project(author=None, filename=None):
1056	"""Creates an dictionary in the style of GSASIIscriptable, for an empty
1057	project.
1058
1059	If no author name or filename is supplied, 'no name' and
1060	<current dir>/test_output.gpx are used , respectively.
1061
1062	Returns: project dictionary, name list
1063
1064	Author: Jackson O'Donnell (jacksonhodonnell .at. gmail.com)
1065	"""
1066	if not filename:
1067	filename = 'test_output.gpx'
1068	filename = os.path.abspath(filename)
1069	gsasii_version = str(GSASIIpath.GetVersionNumber())
1070	LoadG2fil()
1071	try:
1072	import matplotlib as mpl
1073	python_library_versions = G2fil.get_python_versions([mpl, np, sp])
1074	except ImportError:
1075	python_library_versions = G2fil.get_python_versions([np, sp])
1076
1077	controls_data = dict(G2obj.DefaultControls)
1078	controls_data['LastSavedAs'] = filename
1079	controls_data['LastSavedUsing'] = gsasii_version
1080	controls_data['PythonVersions'] = python_library_versions
1081	if author:
1082	controls_data['Author'] = author
1083
1084	output = {'Constraints': {'data': {'HAP': [], 'Hist': [], 'Phase': [],
1085	'Global': []}},
1086	'Controls': {'data': controls_data},
1087	u'Covariance': {'data': {}},
1088	u'Notebook': {'data': ['']},
1089	u'Restraints': {'data': {}},
1090	u'Rigid bodies': {'data': {'RBIds': {'Residue': [], 'Vector': []},
1091	'Residue': {'AtInfo': {}},
1092	'Vector': {'AtInfo': {}}}}}
1093
1094	names = [[u'Notebook'], [u'Controls'], [u'Covariance'],
1095	[u'Constraints'], [u'Restraints'], [u'Rigid bodies']]
1096
1097	return output, names
1098
1099
1100	class G2ImportException(Exception):
1101	pass
1102
1103	class G2ScriptException(Exception):
1104	pass
1105
1106	def import_generic(filename, readerlist, fmthint=None, bank=None):
1107	"""Attempt to import a filename, using a list of reader objects.
1108
1109	Returns the first reader object which worked."""
1110	# Translated from OnImportGeneric method in GSASII.py
1111	primaryReaders, secondaryReaders = [], []
1112	for reader in readerlist:
1113	if fmthint is not None and fmthint not in reader.formatName: continue
1114	flag = reader.ExtensionValidator(filename)
1115	if flag is None:
1116	secondaryReaders.append(reader)
1117	elif flag:
1118	primaryReaders.append(reader)
1119	if not secondaryReaders and not primaryReaders:
1120	raise G2ImportException("Could not read file: ", filename)
1121
1122	with open(filename, 'Ur') as fp:
1123	rd_list = []
1124
1125	for rd in primaryReaders + secondaryReaders:
1126	# Initialize reader
1127	rd.selections = []
1128	if bank is None:
1129	rd.selections = []
1130	else:
1131	rd.selections = [bank-1]
1132	rd.dnames = []
1133	rd.ReInitialize()
1134	# Rewind file
1135	rd.errors = ""
1136	if not rd.ContentsValidator(filename):
1137	# Report error
1138	print("Warning: File {} has a validation error, continuing".format(filename))
1139	if len(rd.selections) > 1:
1140	raise G2ImportException("File {} has {} banks. Specify which bank to read with databank param."
1141	.format(filename,len(rd.selections)))
1142
1143	block = 0
1144	rdbuffer = {}
1145	repeat = True
1146	while repeat:
1147	repeat = False
1148	block += 1
1149	rd.objname = os.path.basename(filename)
1150	try:
1151	flag = rd.Reader(filename,buffer=rdbuffer, blocknum=block)
1152	except:
1153	flag = False
1154	if flag:
1155	# Omitting image loading special cases
1156	rd.readfilename = filename
1157	rd_list.append(copy.deepcopy(rd))
1158	repeat = rd.repeat
1159	else:
1160	if GSASIIpath.GetConfigValue('debug'): print("DBG_{} Reader failed to read {}".format(rd.formatName,filename))
1161	if rd_list:
1162	if rd.warnings:
1163	print("Read warning by", rd.formatName, "reader:",
1164	rd.warnings, file=sys.stderr)
1165	elif bank is None:
1166	print("{} read by Reader {}"
1167	.format(filename,rd.formatName))
1168	else:
1169	print("{} block # {} read by Reader {}"
1170	.format(filename,bank,rd.formatName))
1171	return rd_list
1172	raise G2ImportException("No reader could read file: " + filename)
1173
1174
1175	def load_iprms(instfile, reader, bank=None):
1176	"""Loads instrument parameters from a file, and edits the
1177	given reader.
1178
1179	Returns a 2-tuple of (Iparm1, Iparm2) parameters
1180	"""
1181	LoadG2fil()
1182	ext = os.path.splitext(instfile)[1]
1183
1184	if ext.lower() == '.instprm':
1185	# New GSAS File, load appropriate bank
1186	with open(instfile) as f:
1187	lines = f.readlines()
1188	if bank is None:
1189	bank = reader.powderentry[2]
1190	numbanks = reader.numbanks
1191	iparms = G2fil.ReadPowderInstprm(lines, bank, numbanks, reader)
1192	reader.instfile = instfile
1193	reader.instmsg = '{} (G2 fmt) bank {}'.format(instfile,bank)
1194	return iparms
1195	elif ext.lower() not in ('.prm', '.inst', '.ins'):
1196	raise ValueError('Expected .prm file, found: ', instfile)
1197
1198	# It's an old GSAS file, load appropriately
1199	Iparm = {}
1200	with open(instfile, 'Ur') as fp:
1201	for line in fp:
1202	if '#' in line:
1203	continue
1204	Iparm[line[:12]] = line[12:-1]
1205	ibanks = int(Iparm.get('INS BANK ', '1').strip())
1206	if bank is not None:
1207	# pull out requested bank # bank from the data, and change the bank to 1
1208	Iparm,IparmC = {},Iparm
1209	for key in IparmC:
1210	if 'INS' not in key[:3]: continue #skip around rubbish lines in some old iparm
1211	if key[4:6] == " ":
1212	Iparm[key] = IparmC[key]
1213	elif int(key[4:6].strip()) == bank:
1214	Iparm[key[:4]+' 1'+key[6:]] = IparmC[key]
1215	reader.instbank = bank
1216	elif ibanks == 1:
1217	reader.instbank = 1
1218	else:
1219	raise G2ImportException("Instrument parameter file has {} banks, select one with instbank param."
1220	.format(ibanks))
1221	reader.powderentry[2] = 1
1222	reader.instfile = instfile
1223	reader.instmsg = '{} bank {}'.format(instfile,reader.instbank)
1224	return G2fil.SetPowderInstParms(Iparm, reader)
1225
1226	def load_pwd_from_reader(reader, instprm, existingnames=[],bank=None):
1227	"""Loads powder data from a reader object, and assembles it into a GSASII data tree.
1228
1229	:returns: (name, tree) - 2-tuple of the histogram name (str), and data
1230
1231	Author: Jackson O'Donnell (jacksonhodonnell .at. gmail.com)
1232	"""
1233	HistName = 'PWDR ' + G2obj.StripUnicode(reader.idstring, '_')
1234	HistName = G2obj.MakeUniqueLabel(HistName, existingnames)
1235
1236	try:
1237	Iparm1, Iparm2 = instprm
1238	except ValueError:
1239	Iparm1, Iparm2 = load_iprms(instprm, reader, bank=bank)
1240	print('Instrument parameters read:',reader.instmsg)
1241	Ymin = np.min(reader.powderdata[1])
1242	Ymax = np.max(reader.powderdata[1])
1243	valuesdict = {'wtFactor': 1.0,
1244	'Dummy': False,
1245	'ranId': ran.randint(0, sys.maxsize),
1246	'Offset': [0.0, 0.0], 'delOffset': 0.02*Ymax,
1247	'refOffset': -0.1Ymax, 'refDelt': 0.1Ymax,
1248	'Yminmax': [Ymin, Ymax]}
1249	reader.Sample['ranId'] = valuesdict['ranId']
1250	if 'T' in Iparm1['Type'][0]:
1251	if not reader.clockWd and reader.GSAS:
1252	reader.powderdata[0] *= 100. #put back the CW centideg correction
1253
1254	# Ending keys:
1255	# [u'Reflection Lists',
1256	# u'Limits',
1257	# 'data',
1258	# u'Index Peak List',
1259	# u'Comments',
1260	# u'Unit Cells List',
1261	# u'Sample Parameters',
1262	# u'Peak List',
1263	# u'Background',
1264	# u'Instrument Parameters']
1265	Tmin = np.min(reader.powderdata[0])
1266	Tmax = np.max(reader.powderdata[0])
1267
1268	default_background = [['chebyschev', False, 3, 1.0, 0.0, 0.0],
1269	{'nDebye': 0, 'debyeTerms': [], 'nPeaks': 0, 'peaksList': []}]
1270
1271	output_dict = {u'Reflection Lists': {},
1272	u'Limits': reader.pwdparms.get('Limits', [(Tmin, Tmax), [Tmin, Tmax]]),
1273	u'data': [valuesdict, reader.powderdata, HistName],
1274	u'Index Peak List': [[], []],
1275	u'Comments': reader.comments,
1276	u'Unit Cells List': [],
1277	u'Sample Parameters': reader.Sample,
1278	u'Peak List': {'peaks': [], 'sigDict': {}},
1279	u'Background': reader.pwdparms.get('Background', default_background),
1280	u'Instrument Parameters': [Iparm1, Iparm2],
1281	}
1282
1283	names = [u'Comments',
1284	u'Limits',
1285	u'Background',
1286	u'Instrument Parameters',
1287	u'Sample Parameters',
1288	u'Peak List',
1289	u'Index Peak List',
1290	u'Unit Cells List',
1291	u'Reflection Lists']
1292
1293	# TODO controls?? GSASII.py:1664-7
1294
1295	return HistName, [HistName] + names, output_dict
1296
1297	def _deep_copy_into(from_, into):
1298	"""Helper function for reloading .gpx file. See G2Project.reload()
1299
1300	:author: Jackson O'Donnell (jacksonhodonnell .at. gmail.com)
1301	"""
1302	if isinstance(from_, dict) and isinstance(into, dict):
1303	combined_keys = set(from_.keys()).union(into.keys())
1304	for key in combined_keys:
1305	if key in from_ and key in into:
1306	both_dicts = (isinstance(from_[key], dict)
1307	and isinstance(into[key], dict))
1308	both_lists = (isinstance(from_[key], list)
1309	and isinstance(into[key], list))
1310	if both_dicts or both_lists:
1311	_deep_copy_into(from_[key], into[key])
1312	else:
1313	into[key] = from_[key]
1314	elif key in from_:
1315	into[key] = from_[key]
1316	else: # key in into
1317	del into[key]
1318	elif isinstance(from_, list) and isinstance(into, list):
1319	if len(from_) == len(into):
1320	for i in range(len(from_)):
1321	both_dicts = (isinstance(from_[i], dict)
1322	and isinstance(into[i], dict))
1323	both_lists = (isinstance(from_[i], list)
1324	and isinstance(into[i], list))
1325	if both_dicts or both_lists:
1326	_deep_copy_into(from_[i], into[i])
1327	else:
1328	into[i] = from_[i]
1329	else:
1330	into[:] = from_
1331
1332	def _getCorrImage(ImageReaderlist,proj,imageRef):
1333	'''Gets image & applies dark, background & flat background corrections.
1334	based on :func:`GSASIIimgGUI.GetImageZ`. Expected to be for internal
1335	use only.
1336
1337	:param list ImageReaderlist: list of Reader objects for images
1338	:param object ImageReaderlist: list of Reader objects for images
1339	:param imageRef: A reference to the desired image. Either the Image
1340	tree name (str), the image's index (int) or
1341	a image object (:class:`G2Image`)
1342
1343	:return: array sumImg: corrected image for background/dark/flat back
1344	'''
1345	ImgObj = proj.image(imageRef)
1346	Controls = ImgObj.data['Image Controls']
1347	formatName = Controls.get('formatName','')
1348	imagefile = ImgObj.data['data'][1]
1349	ImageTag = None # fix this for multiimage files
1350	sumImg = G2fil.RereadImageData(ImageReaderlist,imagefile,ImageTag=ImageTag,FormatName=formatName)
1351	if sumImg is None:
1352	return []
1353	darkImg = False
1354	if 'dark image' in Controls:
1355	darkImg,darkScale = Controls['dark image']
1356	if darkImg:
1357	dImgObj = proj.image(darkImg)
1358	formatName = dImgObj.data['Image Controls'].get('formatName','')
1359	imagefile = dImgObj.data['data'][1]
1360	ImageTag = None # fix this for multiimage files
1361	darkImage = G2fil.RereadImageData(ImageReaderlist,imagefile,ImageTag=ImageTag,FormatName=formatName)
1362	if darkImg is None:
1363	raise Exception('Error reading dark image {}'.format(imagefile))
1364	sumImg += np.array(darkImage*darkScale,dtype='int32')
1365	if 'background image' in Controls:
1366	backImg,backScale = Controls['background image']
1367	if backImg: #ignores any transmission effect in the background image
1368	bImgObj = proj.image(backImg)
1369	formatName = bImgObj.data['Image Controls'].get('formatName','')
1370	imagefile = bImgObj.data['data'][1]
1371	ImageTag = None # fix this for multiimage files
1372	backImage = G2fil.RereadImageData(ImageReaderlist,imagefile,ImageTag=ImageTag,FormatName=formatName)
1373	if backImage is None:
1374	raise Exception('Error reading background image {}'.format(imagefile))
1375	if darkImg:
1376	backImage += np.array(darkImage*darkScale/backScale,dtype='int32')
1377	else:
1378	sumImg += np.array(backImage*backScale,dtype='int32')
1379	if 'Gain map' in Controls:
1380	gainMap = Controls['Gain map']
1381	if gainMap:
1382	gImgObj = proj.image(gainMap)
1383	formatName = gImgObj.data['Image Controls'].get('formatName','')
1384	imagefile = gImgObj.data['data'][1]
1385	ImageTag = None # fix this for multiimage files
1386	GMimage = G2fil.RereadImageData(ImageReaderlist,imagefile,ImageTag=ImageTag,FormatName=formatName)
1387	if GMimage is None:
1388	raise Exception('Error reading Gain map image {}'.format(imagefile))
1389	sumImg = sumImg*GMimage/1000
1390	sumImg -= int(Controls.get('Flat Bkg',0))
1391	Imax = np.max(sumImg)
1392	Controls['range'] = [(0,Imax),[0,Imax]]
1393	return np.asarray(sumImg,dtype='int32')
1394
1395	class G2ObjectWrapper(object):
1396	"""Base class for all GSAS-II object wrappers.
1397
1398	The underlying GSAS-II format can be accessed as `wrapper.data`. A number
1399	of overrides are implemented so that the wrapper behaves like a dictionary.
1400
1401	Author: Jackson O'Donnell (jacksonhodonnell .at. gmail.com)
1402	"""
1403	def __init__(self, datadict):
1404	self.data = datadict
1405
1406	def __getitem__(self, key):
1407	return self.data[key]
1408
1409	def __setitem__(self, key, value):
1410	self.data[key] = value
1411
1412	def __contains__(self, key):
1413	return key in self.data
1414
1415	def get(self, k, d=None):
1416	return self.data.get(k, d)
1417
1418	def keys(self):
1419	return self.data.keys()
1420
1421	def values(self):
1422	return self.data.values()
1423
1424	def items(self):
1425	return self.data.items()
1426
1427
1428	class G2Project(G2ObjectWrapper):
1429	"""Represents an entire GSAS-II project.
1430
1431	:param str gpxfile: Existing .gpx file to be loaded. If nonexistent,
1432	creates an empty project.
1433	:param str author: Author's name (not yet implemented)
1434	:param str newgpx: The filename the project should be saved to in
1435	the future. If both newgpx and gpxfile are present, the project is
1436	loaded from the gpxfile, then when saved will be written to newgpx.
1437	:param str filename: Name to be used to save the project. Has same function as
1438	parameter newgpx (do not use both gpxfile and filename). Use of newgpx
1439	is preferred over filename.
1440
1441	There are two ways to initialize this object:
1442
1443	>>> # Load an existing project file
1444	>>> proj = G2Project('filename.gpx')
1445
1446	>>> # Create a new project
1447	>>> proj = G2Project(newgpx='new_file.gpx')
1448
1449	Histograms can be accessed easily.
1450
1451	>>> # By name
1452	>>> hist = proj.histogram('PWDR my-histogram-name')
1453
1454	>>> # Or by index
1455	>>> hist = proj.histogram(0)
1456	>>> assert hist.id == 0
1457
1458	>>> # Or by random id
1459	>>> assert hist == proj.histogram(hist.ranId)
1460
1461	Phases can be accessed the same way.
1462
1463	>>> phase = proj.phase('name of phase')
1464
1465	New data can also be loaded via :meth:`~G2Project.add_phase` and
1466	:meth:`~G2Project.add_powder_histogram`.
1467
1468	>>> hist = proj.add_powder_histogram('some_data_file.chi',
1469	'instrument_parameters.prm')
1470	>>> phase = proj.add_phase('my_phase.cif', histograms=[hist])
1471
1472	Parameters for Rietveld refinement can be turned on and off as well.
1473	See :meth:`~G2Project.set_refinement`, :meth:`~G2Project.clear_refinements`,
1474	:meth:`~G2Project.iter_refinements`, :meth:`~G2Project.do_refinements`.
1475	"""
1476	def __init__(self, gpxfile=None, author=None, filename=None, newgpx=None):
1477	if filename is not None and newgpx is not None:
1478	raise G2ScriptException('Do not use filename and newgpx together')
1479	elif newgpx is not None:
1480	filename = newgpx
1481	if gpxfile is None:
1482	filename = os.path.abspath(os.path.expanduser(filename))
1483	self.filename = filename
1484	self.data, self.names = make_empty_project(author=author, filename=filename)
1485	elif isinstance(gpxfile, str): # TODO: create replacement for isinstance that checks if path exists
1486	# filename is valid, etc.
1487	if isinstance(filename, str):
1488	self.filename = os.path.abspath(os.path.expanduser(filename)) # both are defined
1489	else:
1490	self.filename = os.path.abspath(os.path.expanduser(gpxfile))
1491	# TODO set author
1492	self.data, self.names = LoadDictFromProjFile(gpxfile)
1493	self.update_ids()
1494	else:
1495	raise ValueError("Not sure what to do with gpxfile")
1496
1497	@classmethod
1498	def from_dict_and_names(cls, gpxdict, names, filename=None):
1499	"""Creates a :class:`G2Project` directly from
1500	a dictionary and a list of names. If in doubt, do not use this.
1501
1502	:returns: a :class:`G2Project`
1503	"""
1504	out = cls()
1505	if filename:
1506	filename = os.path.abspath(os.path.expanduser(filename))
1507	out.filename = filename
1508	gpxdict['Controls']['data']['LastSavedAs'] = filename
1509	else:
1510	try:
1511	out.filename = gpxdict['Controls']['data']['LastSavedAs']
1512	except KeyError:
1513	out.filename = None
1514	out.data = gpxdict
1515	out.names = names
1516
1517	def save(self, filename=None):
1518	"""Saves the project, either to the current filename, or to a new file.
1519
1520	Updates self.filename if a new filename provided"""
1521	# TODO update LastSavedUsing ?
1522	if filename:
1523	filename = os.path.abspath(os.path.expanduser(filename))
1524	self.data['Controls']['data']['LastSavedAs'] = filename
1525	self.filename = filename
1526	elif not self.filename:
1527	raise AttributeError("No file name to save to")
1528	SaveDictToProjFile(self.data, self.names, self.filename)
1529
1530	def add_powder_histogram(self, datafile, iparams, phases=[], fmthint=None,
1531	databank=None, instbank=None):
1532	"""Loads a powder data histogram into the project.
1533
1534	Automatically checks for an instrument parameter file, or one can be
1535	provided. Note that in unix fashion, "~" can be used to indicate the
1536	home directory (e.g. ~/G2data/data.fxye).
1537
1538	:param str datafile: The powder data file to read, a filename.
1539	:param str iparams: The instrument parameters file, a filename.
1540	:param list phases: A list of phases to link to the new histogram,
1541	phases can be references by object, name, rId or number.
1542	Alternately, use 'all' to link to all phases in the project.
1543	:param str fmthint: If specified, only importers where the format name
1544	(reader.formatName, as shown in Import menu) contains the
1545	supplied string will be tried as importers. If not specified, all
1546	importers consistent with the file extension will be tried
1547	(equivalent to "guess format" in menu).
1548	:param int databank: Specifies a dataset number to read, if file contains
1549	more than set of data. This should be 1 to read the first bank in
1550	the file (etc.) regardless of the number on the Bank line, etc.
1551	Default is None which means there should only be one dataset in the
1552	file.
1553	:param int instbank: Specifies an instrument parameter set to read, if
1554	the instrument parameter file contains more than set of parameters.
1555	This will match the INS # in an GSAS type file so it will typically
1556	be 1 to read the first parameter set in the file (etc.)
1557	Default is None which means there should only be one parameter set
1558	in the file.
1559
1560	:returns: A :class:`G2PwdrData` object representing
1561	the histogram
1562	"""
1563	LoadG2fil()
1564	datafile = os.path.abspath(os.path.expanduser(datafile))
1565	iparams = os.path.abspath(os.path.expanduser(iparams))
1566	pwdrreaders = import_generic(datafile, Readers['Pwdr'],fmthint=fmthint,bank=databank)
1567	histname, new_names, pwdrdata = load_pwd_from_reader(
1568	pwdrreaders[0], iparams,
1569	[h.name for h in self.histograms()],bank=instbank)
1570	if histname in self.data:
1571	print("Warning - redefining histogram", histname)
1572	elif self.names[-1][0] == 'Phases':
1573	self.names.insert(-1, new_names)
1574	else:
1575	self.names.append(new_names)
1576	self.data[histname] = pwdrdata
1577	self.update_ids()
1578
1579	if phases == 'all':
1580	phases = self.phases()
1581	for phase in phases:
1582	phase = self.phase(phase)
1583	self.link_histogram_phase(histname, phase)
1584
1585	return self.histogram(histname)
1586
1587	def add_simulated_powder_histogram(self, histname, iparams, Tmin, Tmax, Tstep,
1588	wavelength=None, scale=None, phases=[]):
1589	"""Loads a powder data histogram into the project.
1590
1591	Requires an instrument parameter file.
1592	Note that in unix fashion, "~" can be used to indicate the
1593	home directory (e.g. ~/G2data/data.prm). The instrument parameter file
1594	will determine if the histogram is x-ray, CW neutron, TOF, etc. as well
1595	as the instrument type.
1596
1597	:param str histname: A name for the histogram to be created.
1598	:param str iparams: The instrument parameters file, a filename.
1599	:param float Tmin: Minimum 2theta or TOF (ms) for dataset to be simulated
1600	:param float Tmax: Maximum 2theta or TOF (ms) for dataset to be simulated
1601	:param float Tstep: Step size in 2theta or TOF (ms) for dataset to be simulated
1602	:param float wavelength: Wavelength for CW instruments, overriding the value
1603	in the instrument parameters file if specified.
1604	:param float scale: Histogram scale factor which multiplies the pattern. Note that
1605	simulated noise is added to the pattern, so that if the maximum intensity is
1606	small, the noise will mask the computed pattern. The scale
1607	needs to be a large number for CW neutrons.
1608	The default, None, provides a scale of 1 for x-rays and TOF; 10,000 for CW neutrons.
1609	:param list phases: Phases to link to the new histogram. Use proj.phases() to link to
1610	all defined phases.
1611
1612	:returns: A :class:`G2PwdrData` object representing the histogram
1613	"""
1614	LoadG2fil()
1615	iparams = os.path.abspath(os.path.expanduser(iparams))
1616	if not os.path.exists(iparams):
1617	raise G2ScriptException("File does not exist:"+iparams)
1618	rd = G2obj.ImportPowderData( # Initialize a base class reader
1619	extensionlist=tuple(),
1620	strictExtension=False,
1621	formatName = 'Simulate dataset',
1622	longFormatName = 'Compute a simulated pattern')
1623	rd.powderentry[0] = '' # no filename
1624	rd.powderentry[2] = 1 # only one bank
1625	rd.comments.append('This is a dummy dataset for powder pattern simulation')
1626	rd.idstring = histname
1627	#Iparm1, Iparm2 = load_iprms(iparams, rd)
1628	if Tmax < Tmin:
1629	Tmin,Tmax = Tmax,Tmin
1630	Tstep = abs(Tstep)
1631	if 'TOF' in rd.idstring:
1632	N = (np.log(Tmax)-np.log(Tmin))/Tstep
1633	x = np.exp((np.arange(0,N))Tstep+np.log(Tmin1000.))
1634	N = len(x)
1635	else:
1636	N = int((Tmax-Tmin)/Tstep)+1
1637	x = np.linspace(Tmin,Tmax,N,True)
1638	N = len(x)
1639	if N < 3:
1640	raise G2ScriptException("Error: Range is too small or step is too large, <3 points")
1641	rd.powderdata = [
1642	np.array(x), # x-axis values
1643	np.zeros_like(x), # powder pattern intensities
1644	np.ones_like(x), # 1/sig(intensity)^2 values (weights)
1645	np.zeros_like(x), # calc. intensities (zero)
1646	np.zeros_like(x), # calc. background (zero)
1647	np.zeros_like(x), # obs-calc profiles
1648	]
1649	Tmin = rd.powderdata[0][0]
1650	Tmax = rd.powderdata[0][-1]
1651	histname, new_names, pwdrdata = load_pwd_from_reader(rd, iparams,
1652	[h.name for h in self.histograms()])
1653	if histname in self.data:
1654	print("Warning - redefining histogram", histname)
1655	elif self.names[-1][0] == 'Phases':
1656	self.names.insert(-1, new_names)
1657	else:
1658	self.names.append(new_names)
1659	if scale is not None:
1660	pwdrdata['Sample Parameters']['Scale'][0] = scale
1661	elif pwdrdata['Instrument Parameters'][0]['Type'][0].startswith('PNC'):
1662	pwdrdata['Sample Parameters']['Scale'][0] = 10000.
1663	self.data[histname] = pwdrdata
1664	self.update_ids()
1665
1666	for phase in phases:
1667	phase = self.phase(phase)
1668	self.link_histogram_phase(histname, phase)
1669
1670	return self.histogram(histname)
1671
1672	def add_phase(self, phasefile, phasename=None, histograms=[], fmthint=None):
1673	"""Loads a phase into the project from a .cif file
1674
1675	:param str phasefile: The CIF file from which to import the phase.
1676	:param str phasename: The name of the new phase, or None for the default
1677	:param list histograms: The names of the histograms to associate with
1678	this phase. Use proj.histograms() to add to all histograms.
1679	:param str fmthint: If specified, only importers where the format name
1680	(reader.formatName, as shown in Import menu) contains the
1681	supplied string will be tried as importers. If not specified, all
1682	importers consistent with the file extension will be tried
1683	(equivalent to "guess format" in menu).
1684
1685	:returns: A :class:`G2Phase` object representing the
1686	new phase.
1687	"""
1688	LoadG2fil()
1689	histograms = [self.histogram(h).name for h in histograms]
1690	phasefile = os.path.abspath(os.path.expanduser(phasefile))
1691
1692	# TODO handle multiple phases in a file
1693	phasereaders = import_generic(phasefile, Readers['Phase'], fmthint=fmthint)
1694	phasereader = phasereaders[0]
1695
1696	phasename = phasename or phasereader.Phase['General']['Name']
1697	phaseNameList = [p.name for p in self.phases()]
1698	phasename = G2obj.MakeUniqueLabel(phasename, phaseNameList)
1699	phasereader.Phase['General']['Name'] = phasename
1700
1701	if 'Phases' not in self.data:
1702	self.data[u'Phases'] = { 'data': None }
1703	assert phasename not in self.data['Phases'], "phase names should be unique"
1704	self.data['Phases'][phasename] = phasereader.Phase
1705
1706	if phasereader.Constraints:
1707	Constraints = self.data['Constraints']
1708	for i in phasereader.Constraints:
1709	if isinstance(i, dict):
1710	if '_Explain' not in Constraints:
1711	Constraints['_Explain'] = {}
1712	Constraints['_Explain'].update(i)
1713	else:
1714	Constraints['Phase'].append(i)
1715
1716	data = self.data['Phases'][phasename]
1717	generalData = data['General']
1718	SGData = generalData['SGData']
1719	NShkl = len(G2spc.MustrainNames(SGData))
1720	NDij = len(G2spc.HStrainNames(SGData))
1721	Super = generalData.get('Super', 0)
1722	if Super:
1723	SuperVec = np.array(generalData['SuperVec'][0])
1724	else:
1725	SuperVec = []
1726	UseList = data['Histograms']
1727
1728	for hist in histograms:
1729	self.link_histogram_phase(hist, phasename)
1730
1731	for obj in self.names:
1732	if obj[0] == 'Phases':
1733	phasenames = obj
1734	break
1735	else:
1736	phasenames = [u'Phases']
1737	self.names.append(phasenames)
1738	phasenames.append(phasename)
1739
1740	# TODO should it be self.filename, not phasefile?
1741	SetupGeneral(data, os.path.dirname(phasefile))
1742	self.index_ids()
1743
1744	self.update_ids()
1745	return self.phase(phasename)
1746
1747	def link_histogram_phase(self, histogram, phase):
1748	"""Associates a given histogram and phase.
1749
1750	.. seealso::
1751
1752	:meth:`~G2Project.histogram`
1753	:meth:`~G2Project.phase`"""
1754	hist = self.histogram(histogram)
1755	phase = self.phase(phase)
1756
1757	generalData = phase['General']
1758
1759	if hist.name.startswith('HKLF '):
1760	raise NotImplementedError("HKLF not yet supported")
1761	elif hist.name.startswith('PWDR '):
1762	hist['Reflection Lists'][generalData['Name']] = {}
1763	UseList = phase['Histograms']
1764	SGData = generalData['SGData']
1765	NShkl = len(G2spc.MustrainNames(SGData))
1766	NDij = len(G2spc.HStrainNames(SGData))
1767	UseList[hist.name] = SetDefaultDData('PWDR', hist.name, NShkl=NShkl, NDij=NDij)
1768	UseList[hist.name]['hId'] = hist.id
1769	for key, val in [('Use', True), ('LeBail', False),
1770	('newLeBail', True),
1771	('Babinet', {'BabA': [0.0, False],
1772	'BabU': [0.0, False]})]:
1773	if key not in UseList[hist.name]:
1774	UseList[hist.name][key] = val
1775	else:
1776	raise RuntimeError("Unexpected histogram" + hist.name)
1777
1778	def reload(self):
1779	"""Reload self from self.filename"""
1780	data, names = LoadDictFromProjFile(self.filename)
1781	self.names = names
1782	# Need to deep copy the new data file data into the current tree,
1783	# so that any existing G2Phase, or G2PwdrData objects will still be
1784	# valid
1785	_deep_copy_into(from_=data, into=self.data)
1786
1787	def refine(self, newfile=None, printFile=None, makeBack=False):
1788	'''Invoke a refinement for the project. The project is written to
1789	the currently selected gpx file and then either a single or sequential refinement
1790	is performed depending on the setting of 'Seq Data' in Controls
1791	(set in :meth:`get_Controls`).
1792	'''
1793	seqSetting = self.data['Controls']['data'].get('Seq Data',[])
1794	if not seqSetting:
1795	self.index_ids() # index_ids will automatically save the project
1796	# TODO: migrate to RefineCore G2strMain does not properly use printFile
1797	# G2strMain.RefineCore(Controls,Histograms,Phases,restraintDict,rigidbodyDict,parmDict,varyList,
1798	# calcControls,pawleyLookup,ifPrint,printFile,dlg)
1799	G2strMain.Refine(self.filename, makeBack=makeBack)
1800	else:
1801	self._seqrefine()
1802	self.reload() # get file from GPX
1803
1804	def _seqrefine(self):
1805	'''Perform a sequential refinement.
1806	'''
1807
1808	self.data['Controls']['data']['ShowCell'] = True
1809	# add to tree item to project, if not present
1810	if 'Sequential results' not in self.data:
1811	self.data['Sequential results'] = {'data':{}}
1812	self.names.append(['Sequential results'])
1813	self.index_ids() # index_ids will automatically save the project
1814	#GSASIIpath.IPyBreak_base()
1815
1816	# check that constraints are OK
1817	errmsg, warnmsg = G2strIO.ReadCheckConstraints(self.filename)
1818	if errmsg:
1819	print('Refinement error',errmsg)
1820	raise Exception('Constraint error')
1821	if warnmsg:
1822	print(u'Conflict between refinment flag settings and constraints:\n'+
1823	warnmsg+u'\nRefinement not possible')
1824	raise Exception('Constraint error')
1825	OK,Msg = G2strMain.SeqRefine(self.filename,None)
1826
1827	def histogram(self, histname):
1828	"""Returns the histogram named histname, or None if it does not exist.
1829
1830	:param histname: The name of the histogram (str), or ranId or index.
1831	:returns: A :class:`G2PwdrData` object, or None if
1832	the histogram does not exist
1833
1834	.. seealso::
1835	:meth:`~G2Project.histograms`
1836	:meth:`~G2Project.phase`
1837	:meth:`~G2Project.phases`
1838	"""
1839	if isinstance(histname, G2PwdrData):
1840	if histname.proj == self:
1841	return histname
1842	else:
1843	raise Exception('Histogram object (G2PwdrData) is not in current project')
1844	if histname in self.data:
1845	return G2PwdrData(self.data[histname], self)
1846	try:
1847	# see if histname is an id or ranId
1848	histname = int(histname)
1849	except ValueError:
1850	return
1851
1852	for histogram in self.histograms():
1853	if histogram.id == histname or histogram.ranId == histname:
1854	return histogram
1855
1856	def histograms(self, typ=None):
1857	"""Return a list of all histograms, as :class:`G2PwdrData` objects
1858
1859	For now this only finds Powder/Single Xtal histograms, since that is all that is
1860	currently implemented in this module.
1861
1862	:param ste typ: The prefix (type) the histogram such as 'PWDR '. If None
1863	(the default) all known histograms types are found.
1864	:returns: a list of objects
1865
1866	.. seealso::
1867	:meth:`~G2Project.histogram`
1868	:meth:`~G2Project.phase`
1869	:meth:`~G2Project.phases`
1870	"""
1871	output = []
1872	# loop through each tree entry. If it is more than one level (more than one item in the
1873	# list of names). then it must be a histogram, unless labeled Phases or Restraints
1874	if typ is None:
1875	for obj in self.names:
1876	if obj[0].startswith('PWDR ') or obj[0].startswith('HKLF '):
1877	output.append(self.histogram(obj[0]))
1878	else:
1879	for obj in self.names:
1880	if len(obj) > 1 and obj[0].startswith(typ):
1881	output.append(self.histogram(obj[0]))
1882	return output
1883
1884	def phase(self, phasename):
1885	"""
1886	Gives an object representing the specified phase in this project.
1887
1888	:param str phasename: A reference to the desired phase. Either the phase
1889	name (str), the phase's ranId, the phase's index (both int) or
1890	a phase object (:class:`G2Phase`)
1891	:returns: A :class:`G2Phase` object
1892	:raises: KeyError
1893
1894	.. seealso::
1895	:meth:`~G2Project.histograms`
1896	:meth:`~G2Project.phase`
1897	:meth:`~G2Project.phases`
1898	"""
1899	if isinstance(phasename, G2Phase):
1900	if phasename.proj == self:
1901	return phasename
1902	phases = self.data['Phases']
1903	if phasename in phases:
1904	return G2Phase(phases[phasename], phasename, self)
1905
1906	try:
1907	# phasename should be phase index or ranId
1908	phasename = int(phasename)
1909	except ValueError:
1910	return
1911
1912	for phase in self.phases():
1913	if phase.id == phasename or phase.ranId == phasename:
1914	return phase
1915
1916	def phases(self):
1917	"""
1918	Returns a list of all the phases in the project.
1919
1920	:returns: A list of :class:`G2Phase` objects
1921
1922	.. seealso::
1923	:meth:`~G2Project.histogram`
1924	:meth:`~G2Project.histograms`
1925	:meth:`~G2Project.phase`
1926	"""
1927	for obj in self.names:
1928	if obj[0] == 'Phases':
1929	return [self.phase(p) for p in obj[1:]]
1930	return []
1931
1932	def _images(self):
1933	"""Returns a list of all the phases in the project.
1934	"""
1935	return [i[0] for i in self.names if i[0].startswith('IMG ')]
1936
1937	def image(self, imageRef):
1938	"""
1939	Gives an object representing the specified image in this project.
1940
1941	:param str imageRef: A reference to the desired image. Either the Image
1942	tree name (str), the image's index (int) or
1943	a image object (:class:`G2Image`)
1944	:returns: A :class:`G2Image` object
1945	:raises: KeyError
1946
1947	.. seealso::
1948	:meth:`~G2Project.images`
1949	"""
1950	if isinstance(imageRef, G2Image):
1951	if imageRef.proj == self:
1952	return imageRef
1953	else:
1954	raise Exception("Image {} not in current selected project".format(imageRef.name))
1955	if imageRef in self._images():
1956	return G2Image(self.data[imageRef], imageRef, self)
1957
1958	try:
1959	# imageRef should be an index
1960	num = int(imageRef)
1961	imageRef = self._images()[num]
1962	return G2Image(self.data[imageRef], imageRef, self)
1963	except ValueError:
1964	raise Exception("imageRef {} not an object, name or image index in current selected project"
1965	.format(imageRef))
1966	except IndexError:
1967	raise Exception("imageRef {} out of range (max={}) in current selected project"
1968	.format(imageRef,len(self._images())-1))
1969
1970	def images(self):
1971	"""
1972	Returns a list of all the images in the project.
1973
1974	:returns: A list of :class:`G2Image` objects
1975	"""
1976	return [G2Image(self.data[i],i,self) for i in self._images()]
1977
1978	def update_ids(self):
1979	"""Makes sure all phases and histograms have proper hId and pId"""
1980	# Translated from GetUsedHistogramsAndPhasesfromTree,
1981	# GSASIIdataGUI.py:4107
1982	for i, h in enumerate(self.histograms()):
1983	h.id = i
1984	for i, p in enumerate(self.phases()):
1985	p.id = i
1986
1987	def do_refinements(self, refinements, histogram='all', phase='all',
1988	outputnames=None, makeBack=False):
1989	"""Conducts one or a series of refinements according to the
1990	input provided in parameter refinements. This is a wrapper
1991	around :meth:`iter_refinements`
1992
1993	:param list refinements: A list of dictionaries specifiying changes to be made to
1994	parameters before refinements are conducted.
1995	See the :ref:`Refinement_recipe` section for how this is defined.
1996	:param str histogram: Name of histogram for refinements to be applied
1997	to, or 'all'; note that this can be overridden for each refinement
1998	step via a "histograms" entry in the dict.
1999	:param str phase: Name of phase for refinements to be applied to, or
2000	'all'; note that this can be overridden for each refinement
2001	step via a "phases" entry in the dict.
2002	:param list outputnames: Provides a list of project (.gpx) file names
2003	to use for each refinement step (specifying None skips the save step).
2004	See :meth:`save`.
2005	Note that this can be overridden using an "output" entry in the dict.
2006	:param bool makeBack: determines if a backup ).bckX.gpx) file is made
2007	before a refinement is performed. The default is False.
2008
2009	To perform a single refinement without changing any parameters, use this
2010	call:
2011
2012	.. code-block:: python
2013
2014	my_project.do_refinements([])
2015	"""
2016
2017	for proj in self.iter_refinements(refinements, histogram, phase,
2018	outputnames, makeBack):
2019	pass
2020	return self
2021
2022	def iter_refinements(self, refinements, histogram='all', phase='all',
2023	outputnames=None, makeBack=False):
2024	"""Conducts a series of refinements, iteratively. Stops after every
2025	refinement and yields this project, to allow error checking or
2026	logging of intermediate results. Parameter use is the same as for
2027	:meth:`do_refinements` (which calls this method).
2028
2029	>>> def checked_refinements(proj):
2030	... for p in proj.iter_refinements(refs):
2031	... # Track intermediate results
2032	... log(p.histogram('0').residuals)
2033	... log(p.phase('0').get_cell())
2034	... # Check if parameter diverged, nonsense answer, or whatever
2035	... if is_something_wrong(p):
2036	... raise Exception("I need a human!")
2037
2038
2039	"""
2040	if outputnames:
2041	if len(refinements) != len(outputnames):
2042	raise ValueError("Should have same number of outputs to"
2043	"refinements")
2044	else:
2045	outputnames = [None for r in refinements]
2046
2047	for output, refinedict in zip(outputnames, refinements):
2048	if 'histograms' in refinedict:
2049	hist = refinedict['histograms']
2050	else:
2051	hist = histogram
2052	if 'phases' in refinedict:
2053	ph = refinedict['phases']
2054	else:
2055	ph = phase
2056	if 'output' in refinedict:
2057	output = refinedict['output']
2058	self.set_refinement(refinedict, hist, ph)
2059	# Handle 'once' args - refinements that are disabled after this
2060	# refinement
2061	if 'once' in refinedict:
2062	temp = {'set': refinedict['once']}
2063	self.set_refinement(temp, hist, ph)
2064
2065	if output:
2066	self.save(output)
2067
2068	if 'skip' not in refinedict:
2069	self.refine(makeBack=makeBack)
2070	yield self
2071
2072	# Handle 'once' args - refinements that are disabled after this
2073	# refinement
2074	if 'once' in refinedict:
2075	temp = {'clear': refinedict['once']}
2076	self.set_refinement(temp, hist, ph)
2077	if 'call' in refinedict:
2078	fxn = refinedict['call']
2079	if callable(fxn):
2080	fxn(*refinedict.get('callargs',[self]))
2081	elif callable(eval(fxn)):
2082	eval(fxn)(*refinedict.get('callargs',[self]))
2083	else:
2084	raise G2ScriptException("Error: call value {} is not callable".format(fxn))
2085
2086	def set_refinement(self, refinement, histogram='all', phase='all'):
2087	"""Apply specified refinements to a given histogram(s) or phase(s).
2088
2089	:param dict refinement: The refinements to be conducted
2090	:param histogram: Specifies either 'all' (default), a single histogram or
2091	a list of histograms. Histograms may be specified as histogram objects
2092	(see :class:`G2PwdrData`), the histogram name (str) or the index number (int)
2093	of the histogram in the project, numbered starting from 0.
2094	Omitting the parameter or the string 'all' indicates that parameters in
2095	all histograms should be set.
2096	:param phase: Specifies either 'all' (default), a single phase or
2097	a list of phases. Phases may be specified as phase objects
2098	(see :class:`G2Phase`), the phase name (str) or the index number (int)
2099	of the phase in the project, numbered starting from 0.
2100	Omitting the parameter or the string 'all' indicates that parameters in
2101	all phases should be set.
2102
2103	Note that refinement parameters are categorized as one of three types:
2104
2105	1. Histogram parameters
2106	2. Phase parameters
2107	3. Histogram-and-Phase (HAP) parameters
2108
2109	.. seealso::
2110	:meth:`G2PwdrData.set_refinements`
2111	:meth:`G2PwdrData.clear_refinements`
2112	:meth:`G2Phase.set_refinements`
2113	:meth:`G2Phase.clear_refinements`
2114	:meth:`G2Phase.set_HAP_refinements`
2115	:meth:`G2Phase.clear_HAP_refinements`"""
2116
2117	if histogram == 'all':
2118	hists = self.histograms()
2119	elif isinstance(histogram, list) or isinstance(histogram, tuple):
2120	hists = []
2121	for h in histogram:
2122	if isinstance(h, str) or isinstance(h, int):
2123	hists.append(self.histogram(h))
2124	else:
2125	hists.append(h)
2126	elif isinstance(histogram, str) or isinstance(histogram, int):
2127	hists = [self.histogram(histogram)]
2128	else:
2129	hists = [histogram]
2130
2131	if phase == 'all':
2132	phases = self.phases()
2133	elif isinstance(phase, list) or isinstance(phase, tuple):
2134	phases = []
2135	for ph in phase:
2136	if isinstance(ph, str) or isinstance(ph, int):
2137	phases.append(self.phase(ph))
2138	else:
2139	phases.append(ph)
2140	elif isinstance(phase, str) or isinstance(phase, int):
2141	phases = [self.phase(phase)]
2142	else:
2143	phases = [phase]
2144
2145	pwdr_set = {}
2146	phase_set = {}
2147	hap_set = {}
2148	for key, val in refinement.get('set', {}).items():
2149	# Apply refinement options
2150	if G2PwdrData.is_valid_refinement_key(key):
2151	pwdr_set[key] = val
2152	elif G2Phase.is_valid_refinement_key(key):
2153	phase_set[key] = val
2154	elif G2Phase.is_valid_HAP_refinement_key(key):
2155	hap_set[key] = val
2156	else:
2157	raise ValueError("Unknown refinement key", key)
2158
2159	for hist in hists:
2160	hist.set_refinements(pwdr_set)
2161	for phase in phases:
2162	phase.set_refinements(phase_set)
2163	for phase in phases:
2164	phase.set_HAP_refinements(hap_set, hists)
2165
2166	pwdr_clear = {}
2167	phase_clear = {}
2168	hap_clear = {}
2169	for key, val in refinement.get('clear', {}).items():
2170	# Clear refinement options
2171	if G2PwdrData.is_valid_refinement_key(key):
2172	pwdr_clear[key] = val
2173	elif G2Phase.is_valid_refinement_key(key):
2174	phase_clear[key] = val
2175	elif G2Phase.is_valid_HAP_refinement_key(key):
2176	hap_set[key] = val
2177	else:
2178	raise ValueError("Unknown refinement key", key)
2179
2180	for hist in hists:
2181	hist.clear_refinements(pwdr_clear)
2182	for phase in phases:
2183	phase.clear_refinements(phase_clear)
2184	for phase in phases:
2185	phase.clear_HAP_refinements(hap_clear, hists)
2186
2187	def index_ids(self):
2188	self.save()
2189	return G2strIO.GetUsedHistogramsAndPhases(self.filename)
2190
2191	def add_constraint_raw(self, cons_scope, constr):
2192	"""Adds a constraint of type consType to the project.
2193	cons_scope should be one of "Hist", "Phase", "HAP", or "Global".
2194
2195	WARNING it does not check the constraint is well-constructed"""
2196	constrs = self.data['Constraints']['data']
2197	if 'Global' not in constrs:
2198	constrs['Global'] = []
2199	constrs[cons_scope].append(constr)
2200
2201	def hold_many(self, vars, type):
2202	"""Apply holds for all the variables in vars, for constraint of a given type.
2203
2204	type is passed directly to add_constraint_raw as consType
2205
2206	:param list vars: A list of variables to hold. Either :class:`GSASIIobj.G2VarObj` objects,
2207	string variable specifiers, or arguments for :meth:`make_var_obj`
2208	:param str type: A string constraint type specifier. See
2209	:class:`G2Project.add_constraint_raw`
2210
2211	"""
2212	for var in vars:
2213	if isinstance(var, str):
2214	var = self.make_var_obj(var)
2215	elif not isinstance(var, G2obj.G2VarObj):
2216	var = self.make_var_obj(*var)
2217	self.add_constraint_raw(type, [[1.0, var], None, None, 'h'])
2218
2219	def make_var_obj(self, phase=None, hist=None, varname=None, atomId=None,
2220	reloadIdx=True):
2221	"""Wrapper to create a G2VarObj. Takes either a string representation ("p:h:name:a")
2222	or individual names of phase, histogram, varname, and atomId.
2223
2224	Automatically converts string phase, hist, or atom names into the ID required
2225	by G2VarObj."""
2226
2227	if reloadIdx:
2228	self.index_ids()
2229
2230	# If string representation, short circuit
2231	if hist is None and varname is None and atomId is None:
2232	if isinstance(phase, str) and ':' in phase:
2233	return G2obj.G2VarObj(phase)
2234
2235	# Get phase index
2236	phaseObj = None
2237	if isinstance(phase, G2Phase):
2238	phaseObj = phase
2239	phase = G2obj.PhaseRanIdLookup[phase.ranId]
2240	elif phase in self.data['Phases']:
2241	phaseObj = self.phase(phase)
2242	phaseRanId = phaseObj.ranId
2243	phase = G2obj.PhaseRanIdLookup[phaseRanId]
2244
2245	# Get histogram index
2246	if isinstance(hist, G2PwdrData):
2247	hist = G2obj.HistRanIdLookup[hist.ranId]
2248	elif hist in self.data:
2249	histRanId = self.histogram(hist).ranId
2250	hist = G2obj.HistRanIdLookup[histRanId]
2251
2252	# Get atom index (if any)
2253	if isinstance(atomId, G2AtomRecord):
2254	atomId = G2obj.AtomRanIdLookup[phase][atomId.ranId]
2255	elif phaseObj:
2256	atomObj = phaseObj.atom(atomId)
2257	if atomObj:
2258	atomRanId = atomObj.ranId
2259	atomId = G2obj.AtomRanIdLookup[phase][atomRanId]
2260
2261	return G2obj.G2VarObj(phase, hist, varname, atomId)
2262
2263	def add_image(self, imagefile, fmthint=None, defaultImage=None):
2264	"""Load an image into a project
2265
2266	:param str imagefile: The image file to read, a filename.
2267	:param str fmthint: If specified, only importers where the format name
2268	(reader.formatName, as shown in Import menu) contains the
2269	supplied string will be tried as importers. If not specified, all
2270	importers consistent with the file extension will be tried
2271	(equivalent to "guess format" in menu).
2272	:param str defaultImage: The name of an image to use as a default for
2273	setting parameters for the image file to read.
2274
2275	:returns: a list of G2Image object for the added image(s) [this routine
2276	has not yet been tested with files with multiple images...]
2277	"""
2278	LoadG2fil()
2279	imagefile = os.path.abspath(os.path.expanduser(imagefile))
2280	readers = import_generic(imagefile, Readers['Image'], fmthint=fmthint)
2281	objlist = []
2282	for rd in readers:
2283	if rd.SciPy: #was default read by scipy; needs 1 time fixes
2284	print('TODO: Image {} read by SciPy. Parameters likely need editing'.format(imagefile))
2285	#see this: G2IO.EditImageParms(self,rd.Data,rd.Comments,rd.Image,imagefile)
2286	rd.SciPy = False
2287	rd.readfilename = imagefile
2288	if rd.repeatcount == 1 and not rd.repeat: # skip image number if only one in set
2289	rd.Data['ImageTag'] = None
2290	else:
2291	rd.Data['ImageTag'] = rd.repeatcount
2292	rd.Data['formatName'] = rd.formatName
2293	if rd.sumfile:
2294	rd.readfilename = rd.sumfile
2295	# Load generic metadata, as configured
2296	G2fil.GetColumnMetadata(rd)
2297	# Code from G2IO.LoadImage2Tree(rd.readfilename,self,rd.Comments,rd.Data,rd.Npix,rd.Image)
2298	Imax = np.amax(rd.Image)
2299	ImgNames = [i[0] for i in self.names if i[0].startswith('IMG ')]
2300	TreeLbl = 'IMG '+os.path.basename(imagefile)
2301	ImageTag = rd.Data.get('ImageTag')
2302	if ImageTag:
2303	TreeLbl += ' #'+'%04d'%(ImageTag)
2304	imageInfo = (imagefile,ImageTag)
2305	else:
2306	imageInfo = imagefile
2307	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
2308	# MT dict to contain image info
2309	ImgDict = {}
2310	ImgDict['data'] = [rd.Npix,imageInfo]
2311	ImgDict['Comments'] = rd.Comments
2312	if defaultImage:
2313	if isinstance(defaultImage, G2Image):
2314	if defaultImage.proj == self:
2315	defaultImage = self.data[defaultImage.name]['data']
2316	else:
2317	raise Exception("Image {} not in current selected project".format(defaultImage.name))
2318	elif defaultImage in self._images():
2319	defaultImage = self.data[defaultImage]['data']
2320	else:
2321	defaultImage = None
2322	Data = rd.Data
2323	if defaultImage:
2324	Data = copy.copy(defaultImage)
2325	Data['showLines'] = True
2326	Data['ring'] = []
2327	Data['rings'] = []
2328	Data['cutoff'] = 10.
2329	Data['pixLimit'] = 20
2330	Data['edgemin'] = 100000000
2331	Data['calibdmin'] = 0.5
2332	Data['calibskip'] = 0
2333	Data['ellipses'] = []
2334	Data['calibrant'] = ''
2335	Data['GonioAngles'] = [0.,0.,0.]
2336	Data['DetDepthRef'] = False
2337	else:
2338	Data['type'] = 'PWDR'
2339	Data['color'] = GSASIIpath.GetConfigValue('Contour_color','Paired')
2340	if 'tilt' not in Data: #defaults if not preset in e.g. Bruker importer
2341	Data['tilt'] = 0.0
2342	Data['rotation'] = 0.0
2343	Data['pixLimit'] = 20
2344	Data['calibdmin'] = 0.5
2345	Data['cutoff'] = 10.
2346	Data['showLines'] = False
2347	Data['calibskip'] = 0
2348	Data['ring'] = []
2349	Data['rings'] = []
2350	Data['edgemin'] = 100000000
2351	Data['ellipses'] = []
2352	Data['GonioAngles'] = [0.,0.,0.]
2353	Data['DetDepth'] = 0.
2354	Data['DetDepthRef'] = False
2355	Data['calibrant'] = ''
2356	Data['IOtth'] = [5.0,50.0]
2357	Data['LRazimuth'] = [0.,180.]
2358	Data['azmthOff'] = 0.0
2359	Data['outChannels'] = 2500
2360	Data['outAzimuths'] = 1
2361	Data['centerAzm'] = False
2362	Data['fullIntegrate'] = GSASIIpath.GetConfigValue('fullIntegrate',True)
2363	Data['setRings'] = False
2364	Data['background image'] = ['',-1.0]
2365	Data['dark image'] = ['',-1.0]
2366	Data['Flat Bkg'] = 0.0
2367	Data['Oblique'] = [0.5,False]
2368	Data['setDefault'] = False
2369	Data['range'] = [(0,Imax),[0,Imax]]
2370	ImgDict['Image Controls'] = Data
2371	ImgDict['Masks'] = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],
2372	'Frames':[],'Thresholds':[(0,Imax),[0,Imax]]}
2373	ImgDict['Stress/Strain'] = {'Type':'True','d-zero':[],'Sample phi':0.0,
2374	'Sample z':0.0,'Sample load':0.0}
2375	self.names.append([TreeName]+['Comments','Image Controls','Masks','Stress/Strain'])
2376	self.data[TreeName] = ImgDict
2377	del rd.Image
2378	objlist.append(G2Image(self.data[TreeName], TreeName, self))
2379	return objlist
2380
2381	def get_Controls(self, control):
2382	'''Return project controls settings
2383
2384	:param str control: the item to be returned. See below for allowed values.
2385	:returns: The value for the control.
2386
2387	Allowed values for parameter control:
2388
2389	* cycles: the maximum number of cycles (returns int)
2390	* sequential: the histograms used for a sequential refinement as a list
2391	of histogram names or an empty list when in non-sequential mode.
2392	* seqCopy: returns True or False. True indicates that results from
2393	each sequential fit are used as the starting point for the next
2394	histogram.
2395	* Anything else returns the value in the Controls dict, if present. An
2396	exception is raised if the control value is not present.
2397
2398	.. seealso::
2399	:meth:`set_Controls`
2400	'''
2401	if control == 'cycles':
2402	return self.data['Controls']['data']['max cyc']
2403	elif control == 'sequential':
2404	return self.data['Controls']['data']['Seq Data']
2405	elif control in self.data['Controls']['data']:
2406	return self.data['Controls']['data'][control]
2407	elif control == 'seqCopy':
2408	return self.data['Controls']['data']['Copy2Next']
2409	else:
2410	print('Defined Controls:',self.data['Controls']['data'].keys())
2411	raise Exception('{} is an invalid control value'.format(control))
2412
2413	def set_Controls(self, control, value):
2414	'''Set project controls
2415
2416	:param str control: the item to be set. See below for allowed values.
2417	:param value: the value to be set.
2418
2419	Allowed values for parameter control:
2420
2421	* cycles: sets the maximum number of cycles (value must be int)
2422	* sequential: sets the histograms to be used for a sequential refinement.
2423	Use an empty list to turn off sequential fitting.
2424	The values in the list may be the name of the histogram (a str), or
2425	a ranId or index (int values), see :meth:`histogram`.
2426	* seqCopy: when True, the results from each sequential fit are used as
2427	the starting point for the next. After each fit is is set to False.
2428	Ignored for non-sequential fits.
2429
2430	.. seealso::
2431	:meth:`get_Controls`
2432	'''
2433	if control == 'cycles':
2434	self.data['Controls']['data']['max cyc'] = int(value)
2435	elif control == 'seqCopy':
2436	self.data['Controls']['data']['Copy2Next'] = bool(value)
2437	elif control == 'sequential':
2438	histlist = []
2439	for i,j in enumerate(value):
2440	h = self.histogram(j)
2441	if h:
2442	histlist.append(h.name)
2443	else:
2444	raise Exception('item #{} ({}) is an invalid histogram value'
2445	.format(i,j))
2446	self.data['Controls']['data']['Seq Data'] = histlist
2447	else:
2448	raise Exception('{} is an invalid control value'.format(control))
2449
2450	def copyHistParms(self,sourcehist,targethistlist='all',modelist='all'):
2451	'''Copy histogram information from one histogram to others
2452
2453	:param sourcehist: is a histogram object (:class:`G2PwdrData`) or
2454	a histogram name or the index number of the histogram
2455	:param list targethistlist: a list of histograms where each item in the
2456	list can be a histogram object (:class:`G2PwdrData`),
2457	a histogram name or the index number of the histogram.
2458	if the string 'all' (default value), then all histograms in
2459	the project are used.
2460	:param list modelist: May be a list of sections to copy, which may
2461	include 'Background', 'Instrument Parameters', 'Limits' and
2462	'Sample Parameters' (items may be shortened to uniqueness and
2463	capitalization is ignored, so ['b','i','L','s'] will work.)
2464	The default value, 'all' causes the listed sections to
2465
2466	'''
2467	sections = ('Background','Instrument Parameters','Limits',
2468	'Sample Parameters')
2469	hist_in = self.histogram(sourcehist)
2470	if not hist_in:
2471	raise Exception('{} is not a valid histogram'.format(sourcehist))
2472	if targethistlist == "all":
2473	targethistlist = self.histograms()
2474	if 'all' in modelist:
2475	copysections = sections
2476	else:
2477	copysections = set()
2478	for s in sections:
2479	for m in modelist:
2480	if s.lower().startswith(m.lower()):
2481	copysections.add(s)
2482	for h in targethistlist:
2483	hist_out = self.histogram(h)
2484	if not hist_out:
2485	raise Exception('{} is not a valid histogram'.format(h))
2486	for key in copysections:
2487	hist_out[key] = copy.deepcopy(hist_in[key])
2488
2489	class G2AtomRecord(G2ObjectWrapper):
2490	"""Wrapper for an atom record. Has convenient accessors via @property.
2491
2492
2493	Available accessors: label, type, refinement_flags, coordinates,
2494	occupancy, ranId, id, adp_flag, uiso
2495
2496	Example:
2497
2498	>>> atom = some_phase.atom("O3")
2499	>>> # We can access the underlying data format
2500	>>> atom.data
2501	['O3', 'O-2', '', ... ]
2502	>>> # We can also use wrapper accessors
2503	>>> atom.coordinates
2504	(0.33, 0.15, 0.5)
2505	>>> atom.refinement_flags
2506	u'FX'
2507	>>> atom.ranId
2508	4615973324315876477
2509	>>> atom.occupancy
2510	1.0
2511	"""
2512	def __init__(self, data, indices, proj):
2513	self.data = data
2514	self.cx, self.ct, self.cs, self.cia = indices
2515	self.proj = proj
2516
2517	@property
2518	def label(self):
2519	'''Get the associated atom's label
2520	'''
2521	return self.data[self.ct-1]
2522
2523	@property
2524	def type(self):
2525	'''Get the associated atom's type
2526	'''
2527	return self.data[self.ct]
2528
2529	@property
2530	def refinement_flags(self):
2531	'''Get or set refinement flags for the associated atom
2532	'''
2533	return self.data[self.ct+1]
2534
2535	@refinement_flags.setter
2536	def refinement_flags(self, other):
2537	# Automatically check it is a valid refinement
2538	for c in other:
2539	if c not in ' FXU':
2540	raise ValueError("Invalid atom refinement: ", other)
2541	self.data[self.ct+1] = other
2542
2543	@property
2544	def coordinates(self):
2545	'''Get the associated atom's coordinates
2546	'''
2547	return tuple(self.data[self.cx:self.cx+3])
2548
2549	@property
2550	def occupancy(self):
2551	'''Get or set the associated atom's occupancy fraction
2552	'''
2553	return self.data[self.cx+3]
2554
2555	@occupancy.setter
2556	def occupancy(self, val):
2557	self.data[self.cx+3] = float(val)
2558
2559	@property
2560	def ranId(self):
2561	'''Get the associated atom's Random Id number
2562	'''
2563	return self.data[self.cia+8]
2564
2565	@property
2566	def adp_flag(self):
2567	'''Get the associated atom's iso/aniso setting, 'I' or 'A'
2568	'''
2569	# Either 'I' or 'A'
2570	return self.data[self.cia]
2571
2572	@property
2573	def uiso(self):
2574	'''Get or set the associated atom's Uiso or Uaniso value(s)
2575	'''
2576	if self.adp_flag == 'I':
2577	return self.data[self.cia+1]
2578	else:
2579	return self.data[self.cia+2:self.cia+8]
2580
2581	@uiso.setter
2582	def uiso(self, value):
2583	if self.adp_flag == 'I':
2584	self.data[self.cia+1] = float(value)
2585	else:
2586	assert len(value) == 6
2587	self.data[self.cia+2:self.cia+8] = [float(v) for v in value]
2588
2589	class G2PwdrData(G2ObjectWrapper):
2590	"""Wraps a Powder Data Histogram."""
2591	def __init__(self, data, proj):
2592	self.data = data
2593	self.proj = proj
2594
2595	@staticmethod
2596	def is_valid_refinement_key(key):
2597	valid_keys = ['Limits', 'Sample Parameters', 'Background',
2598	'Instrument Parameters']
2599	return key in valid_keys
2600
2601	@property
2602	def name(self):
2603	return self.data['data'][-1]
2604
2605	@property
2606	def ranId(self):
2607	return self.data['data'][0]['ranId']
2608
2609	@property
2610	def residuals(self):
2611	'''Provides a dictionary with with the R-factors for this histogram.
2612	Includes the weighted and unweighted profile terms (R, Rb, wR, wRb, wRmin)
2613	as well as the Bragg R-values for each phase (ph:H:Rf and ph:H:Rf^2).
2614	'''
2615	data = self.data['data'][0]
2616	return {key: data[key] for key in data
2617	if key in ['R', 'Rb', 'wR', 'wRb', 'wRmin']
2618	or ':' in key}
2619
2620	@property
2621	def InstrumentParameters(self):
2622	'''Provides a dictionary with with the Instrument Parameters
2623	for this histogram.
2624	'''
2625	return self.data['Instrument Parameters'][0]
2626
2627	@property
2628	def SampleParameters(self):
2629	'''Provides a dictionary with with the Sample Parameters
2630	for this histogram.
2631	'''
2632	return self.data['Sample Parameters']
2633
2634	@property
2635	def Background(self):
2636	'''Provides a list with with the Background parameters
2637	for this histogram.
2638
2639	:returns: list containing a list and dict with background values
2640	'''
2641	return self.data['Background']
2642
2643	def add_back_peak(self,pos,int,sig,gam,refflags=[]):
2644	'''Adds a background peak to the Background parameters
2645
2646	:param float pos: position of peak, a 2theta or TOF value
2647	:param float int: integrated intensity of background peak, usually large
2648	:param float sig: Gaussian width of background peak, usually large
2649	:param float gam: Lorentzian width of background peak, usually unused (small)
2650	:param list refflags: a list of 1 to 4 boolean refinement flags for
2651	pos,int,sig & gam, respectively (use [0,1] to refine int only).
2652	Defaults to [] which means nothing is refined.
2653	'''
2654	if 'peaksList' not in self.Background[1]:
2655	self.Background[1]['peaksList'] = []
2656	flags = 4*[False]
2657	for i,f in enumerate(refflags):
2658	if i>3: break
2659	flags[i] = bool(f)
2660	bpk = []
2661	for i,j in zip((pos,int,sig,gam),flags):
2662	bpk += [float(i),j]
2663	self.Background[1]['peaksList'].append(bpk)
2664	self.Background[1]['nPeaks'] = len(self.Background[1]['peaksList'])
2665
2666	def del_back_peak(self,peaknum):
2667	'''Removes a background peak from the Background parameters
2668
2669	:param int peaknum: the number of the peak (starting from 0)
2670	'''
2671	npks = self.Background[1].get('nPeaks',0)
2672	if peaknum >= npks:
2673	raise Exception('peak {} not found in histogram {}'.format(peaknum,self.name))
2674	del self.Background[1]['peaksList'][peaknum]
2675	self.Background[1]['nPeaks'] = len(self.Background[1]['peaksList'])
2676
2677	def ref_back_peak(self,peaknum,refflags=[]):
2678	'''Sets refinement flag for a background peak
2679
2680	:param int peaknum: the number of the peak (starting from 0)
2681	:param list refflags: a list of 1 to 4 boolean refinement flags for
2682	pos,int,sig & gam, respectively. If a flag is not specified
2683	it defaults to False (use [0,1] to refine int only).
2684	Defaults to [] which means nothing is refined.
2685	'''
2686	npks = self.Background[1].get('nPeaks',0)
2687	if peaknum >= npks:
2688	raise Exception('peak {} not found in histogram {}'.format(peaknum,self.name))
2689	flags = 4*[False]
2690	for i,f in enumerate(refflags):
2691	if i>3: break
2692	flags[i] = bool(f)
2693	for i,f in enumerate(flags):
2694	self.Background[1]['peaksList'][peaknum][2*i+1] = f
2695
2696	@property
2697	def id(self):
2698	self.proj.update_ids()
2699	return self.data['data'][0]['hId']
2700
2701	@id.setter
2702	def id(self, val):
2703	self.data['data'][0]['hId'] = val
2704
2705	def fit_fixed_points(self):
2706	"""Attempts to apply a background fit to the fixed points currently specified."""
2707	def SetInstParms(Inst):
2708	dataType = Inst['Type'][0]
2709	insVary = []
2710	insNames = []
2711	insVals = []
2712	for parm in Inst:
2713	insNames.append(parm)
2714	insVals.append(Inst[parm][1])
2715	if parm in ['U','V','W','X','Y','Z','SH/L','I(L2)/I(L1)','alpha',
2716	'beta-0','beta-1','beta-q','sig-0','sig-1','sig-2','sig-q',] and Inst[parm][2]:
2717	Inst[parm][2] = False
2718	instDict = dict(zip(insNames, insVals))
2719	instDict['X'] = max(instDict['X'], 0.01)
2720	instDict['Y'] = max(instDict['Y'], 0.01)
2721	if 'SH/L' in instDict:
2722	instDict['SH/L'] = max(instDict['SH/L'], 0.002)
2723	return dataType, instDict, insVary
2724
2725	bgrnd = self.data['Background']
2726
2727	# Need our fixed points in order
2728	bgrnd[1]['FixedPoints'].sort(key=lambda pair: pair[0])
2729	X = [x for x, y in bgrnd[1]['FixedPoints']]
2730	Y = [y for x, y in bgrnd[1]['FixedPoints']]
2731
2732	limits = self.data['Limits'][1]
2733	if X[0] > limits[0]:
2734	X = [limits[0]] + X
2735	Y = [Y[0]] + Y
2736	if X[-1] < limits[1]:
2737	X += [limits[1]]
2738	Y += [Y[-1]]
2739
2740	# Some simple lookups
2741	controls = self.proj['Controls']['data']
2742	inst, inst2 = self.data['Instrument Parameters']
2743	pwddata = self.data['data'][1]
2744
2745	# Construct the data for background fitting
2746	xBeg = np.searchsorted(pwddata[0], limits[0])
2747	xFin = np.searchsorted(pwddata[0], limits[1])
2748	xdata = pwddata[0][xBeg:xFin]
2749	ydata = si.interp1d(X,Y)(ma.getdata(xdata))
2750
2751	W = [1]*len(xdata)
2752	Z = [0]*len(xdata)
2753
2754	dataType, insDict, insVary = SetInstParms(inst)
2755	bakType, bakDict, bakVary = G2pwd.SetBackgroundParms(bgrnd)
2756
2757	# Do the fit
2758	data = np.array([xdata, ydata, W, Z, Z, Z])
2759	G2pwd.DoPeakFit('LSQ', [], bgrnd, limits, inst, inst2, data,
2760	prevVaryList=bakVary, controls=controls)
2761
2762	# Post-fit
2763	parmDict = {}
2764	bakType, bakDict, bakVary = G2pwd.SetBackgroundParms(bgrnd)
2765	parmDict.update(bakDict)
2766	parmDict.update(insDict)
2767	pwddata[3][xBeg:xFin] *= 0
2768	pwddata[5][xBeg:xFin] *= 0
2769	pwddata[4][xBeg:xFin] = G2pwd.getBackground('', parmDict, bakType, dataType, xdata)[0]
2770
2771	# TODO adjust pwddata? GSASIIpwdGUI.py:1041
2772	# TODO update background
2773	self.proj.save()
2774
2775	def getdata(self,datatype):
2776	'''Provides access to the histogram data of the selected data type
2777
2778	:param str datatype: must be one of the following values (case is ignored)
2779
2780	* 'X': the 2theta or TOF values for the pattern
2781	* 'Yobs': the observed intensity values
2782	* 'Yweight': the weights for each data point (1/sigma**2)
2783	* 'Ycalc': the computed intensity values
2784	* 'Background': the computed background values
2785	* 'Residual': the difference between Yobs and Ycalc (obs-calc)
2786
2787	:returns: an numpy MaskedArray with data values of the requested type
2788
2789	'''
2790	enums = ['x', 'yobs', 'yweight', 'ycalc', 'background', 'residual']
2791	if datatype.lower() not in enums:
2792	raise G2ScriptException("Invalid datatype = "+datatype+" must be one of "+str(enums))
2793	return self.data['data'][1][enums.index(datatype.lower())]
2794
2795	def y_calc(self):
2796	return self.data['data'][1][3]
2797
2798	def Export(self,fileroot,extension):
2799	'''Write the histogram into a file. The path is specified by fileroot and
2800	extension.
2801
2802	:param str fileroot: name of the file, optionally with a path (extension is
2803	ignored)
2804	:param str extension: includes '.', must match an extension in global
2805	exportersByExtension['powder'] or a Exception is raised.
2806	:returns: name of file that was written
2807	'''
2808	if extension not in exportersByExtension.get('powder',[]):
2809	raise G2ScriptException('No Writer for file type = "'+extension+'"')
2810	fil = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
2811	obj = exportersByExtension['powder'][extension]
2812	obj.SetFromArray(hist=self.data,histname=self.name)
2813	obj.Writer(self.name,fil)
2814
2815	def plot(self, Yobs=True, Ycalc=True, Background=True, Residual=True):
2816	try:
2817	import matplotlib.pyplot as plt
2818	except ImportError:
2819	print('Unable to import matplotlib, skipping plot')
2820	return
2821	data = self.data['data'][1]
2822	if Yobs:
2823	plt.plot(data[0], data[1], label='Yobs')
2824	if Ycalc:
2825	plt.plot(data[0], data[3], label='Ycalc')
2826	if Background:
2827	plt.plot(data[0], data[4], label='Background')
2828	if Residual:
2829	plt.plot(data[0], data[5], label="Residual")
2830
2831	def get_wR(self):
2832	"""returns the overall weighted profile R factor for a histogram
2833
2834	:returns: a wR value as a percentage or None if not defined
2835	"""
2836	return self['data'][0].get('wR')
2837
2838	def set_refinements(self, refs):
2839	"""Sets the histogram refinement parameter 'key' to the specification 'value'.
2840
2841	:param dict refs: A dictionary of the parameters to be set. See the
2842	:ref:`Histogram_parameters_table` table for a description of
2843	what these dictionaries should be.
2844
2845	:returns: None
2846
2847	"""
2848	do_fit_fixed_points = False
2849	for key, value in refs.items():
2850	if key == 'Limits':
2851	old_limits = self.data['Limits'][1]
2852	new_limits = value
2853	if isinstance(new_limits, dict):
2854	if 'low' in new_limits:
2855	old_limits[0] = new_limits['low']
2856	if 'high' in new_limits:
2857	old_limits[1] = new_limits['high']
2858	else:
2859	old_limits[0], old_limits[1] = new_limits
2860	elif key == 'Sample Parameters':
2861	sample = self.data['Sample Parameters']
2862	for sparam in value:
2863	if sparam not in sample:
2864	raise ValueError("Unknown refinement parameter, "
2865	+ str(sparam))
2866	sample[sparam][1] = True
2867	elif key == 'Background':
2868	bkg, peaks = self.data['Background']
2869
2870	# If True or False, just set the refine parameter
2871	if value in (True, False):
2872	bkg[1] = value
2873	return
2874
2875	if 'type' in value:
2876	bkg[0] = value['type']
2877	if 'refine' in value:
2878	bkg[1] = value['refine']
2879	if 'no. coeffs' in value:
2880	cur_coeffs = bkg[2]
2881	n_coeffs = value['no. coeffs']
2882	if n_coeffs > cur_coeffs:
2883	for x in range(n_coeffs - cur_coeffs):
2884	bkg.append(0.0)
2885	else:
2886	for _ in range(cur_coeffs - n_coeffs):
2887	bkg.pop()
2888	bkg[2] = n_coeffs
2889	if 'coeffs' in value:
2890	bkg[3:] = value['coeffs']
2891	if 'FixedPoints' in value:
2892	peaks['FixedPoints'] = [(float(a), float(b))
2893	for a, b in value['FixedPoints']]
2894	if value.get('fit fixed points', False):
2895	do_fit_fixed_points = True
2896	if 'peaks' in value:
2897	for i,flags in enumerate(value['peaks']):
2898	self.ref_back_peak(i,flags)
2899
2900	elif key == 'Instrument Parameters':
2901	instrument, secondary = self.data['Instrument Parameters']
2902	for iparam in value:
2903	try:
2904	instrument[iparam][2] = True
2905	except IndexError:
2906	raise ValueError("Invalid key:", iparam)
2907	else:
2908	raise ValueError("Unknown key:", key)
2909	# Fit fixed points after the fact - ensure they are after fixed points
2910	# are added
2911	if do_fit_fixed_points:
2912	# Background won't be fit if refinement flag not set
2913	orig = self.data['Background'][0][1]
2914	self.data['Background'][0][1] = True
2915	self.fit_fixed_points()
2916	# Restore the previous value
2917	self.data['Background'][0][1] = orig
2918
2919	def clear_refinements(self, refs):
2920	"""Clears the refinement parameter 'key' and its associated value.
2921
2922	:param dict refs: A dictionary of parameters to clear.
2923	See the :ref:`Histogram_parameters_table` table for what can be specified.
2924	"""
2925	for key, value in refs.items():
2926	if key == 'Limits':
2927	old_limits, cur_limits = self.data['Limits']
2928	cur_limits[0], cur_limits[1] = old_limits
2929	elif key == 'Sample Parameters':
2930	sample = self.data['Sample Parameters']
2931	for sparam in value:
2932	sample[sparam][1] = False
2933	elif key == 'Background':
2934	bkg, peaks = self.data['Background']
2935
2936	# If True or False, just set the refine parameter
2937	if value in (True, False):
2938	bkg[1] = False
2939	return
2940
2941	bkg[1] = False
2942	if 'FixedPoints' in value:
2943	if 'FixedPoints' in peaks:
2944	del peaks['FixedPoints']
2945	if 'peaks' in value:
2946	for i in range(len(self.Background[1]['peaksList'])):
2947	self.ref_back_peak(i,[])
2948	elif key == 'Instrument Parameters':
2949	instrument, secondary = self.data['Instrument Parameters']
2950	for iparam in value:
2951	instrument[iparam][2] = False
2952	else:
2953	raise ValueError("Unknown key:", key)
2954
2955	def add_peak(self,area,dspace=None,Q=None,ttheta=None):
2956	'''Adds a single peak to the peak list
2957	:param float area: peak area
2958	:param float dspace: peak position as d-space (A)
2959	:param float Q: peak position as Q (A-1)
2960	:param float ttheta: peak position as 2Theta (deg)
2961
2962	Note: only one of the parameters dspace, Q or ttheta may be specified
2963	'''
2964	import GSASIIlattice as G2lat
2965	import GSASIImath as G2mth
2966	if (not dspace) + (not Q) + (not ttheta) != 2:
2967	print('add_peak error: too many or no peak position(s) specified')
2968	return
2969	pos = ttheta
2970	Parms,Parms2 = self.data['Instrument Parameters']
2971	if Q:
2972	pos = G2lat.Dsp2pos(Parms,2.*np.pi/Q)
2973	elif dspace:
2974	pos = G2lat.Dsp2pos(Parms,dspace)
2975	peaks = self.data['Peak List']
2976	peaks['sigDict'] = {} #no longer valid
2977	peaks['peaks'].append(G2mth.setPeakparms(Parms,Parms2,pos,area))
2978
2979	def set_peakFlags(self,peaklist=None,area=None,pos=None,sig=None,gam=None):
2980	'''Set refinement flags for peaks
2981
2982	:param list peaklist: a list of peaks to change flags. If None (default), changes
2983	are made to all peaks.
2984	:param bool area: Sets or clears the refinement flag for the peak area value.
2985	If None (the default), no change is made.
2986	:param bool pos: Sets or clears the refinement flag for the peak position value.
2987	If None (the default), no change is made.
2988	:param bool sig: Sets or clears the refinement flag for the peak sig (Gaussian width) value.
2989	If None (the default), no change is made.
2990	:param bool gam: Sets or clears the refinement flag for the peak sig (Lorentzian width) value.
2991	If None (the default), no change is made.
2992
2993	Note that when peaks are first created the area flag is on and the other flags are
2994	initially off.
2995
2996	Example::
2997
2998	set_peakFlags(sig=False,gam=True)
2999
3000	causes the sig refinement flag to be cleared and the gam flag to be set, in both cases for
3001	all peaks. The position and area flags are not changed from their previous values.
3002	'''
3003	peaks = self.data['Peak List']
3004	if peaklist is None:
3005	peaklist = range(len(peaks['peaks']))
3006	for i in peaklist:
3007	for var,j in [(area,3),(pos,1),(sig,5),(gam,7)]:
3008	if var is not None:
3009	peaks['peaks'][i][j] = var
3010
3011	def refine_peaks(self):
3012	'''Causes a refinement of peak position, background and instrument parameters
3013	'''
3014	import GSASIIpwd as G2pwd
3015	controls = self.proj.data.get('Controls',{})
3016	controls = controls.get('data',
3017	{'deriv type':'analytic','min dM/M':0.001,} #fill in defaults if needed
3018	)
3019	peaks = self.data['Peak List']
3020	Parms,Parms2 = self.data['Instrument Parameters']
3021	background = self.data['Background']
3022	limits = self.data['Limits'][1]
3023	bxye = np.zeros(len(self.data['data'][1][1]))
3024	peaks['sigDict'] = G2pwd.DoPeakFit('LSQ',peaks['peaks'],background,limits,
3025	Parms,Parms2,self.data['data'][1],bxye,[],
3026	False,controls,None)[0]
3027
3028	def SaveProfile(self,filename):
3029	'''Writes a GSAS-II (new style) .instprm file
3030	'''
3031	data,Parms2 = self.data['Instrument Parameters']
3032	filename = os.path.splitext(filename)[0]+'.instprm' # make sure extension is .instprm
3033	File = open(filename,'w')
3034	File.write("#GSAS-II instrument parameter file; do not add/delete items!\n")
3035	for item in data:
3036	File.write(item+':'+str(data[item][1])+'\n')
3037	File.close()
3038	print ('Instrument parameters saved to: '+filename)
3039
3040	def LoadProfile(self,filename,bank=0):
3041	'''Reads a GSAS-II (new style) .instprm file and overwrites the current
3042	parameters
3043
3044	:param str filename: instrument parameter file name, extension ignored if not
3045	.instprm
3046	:param int bank: bank number to read, defaults to zero
3047	'''
3048	filename = os.path.splitext(filename)[0]+'.instprm' # make sure extension is .instprm
3049	File = open(filename,'r')
3050	S = File.readline()
3051	newItems = []
3052	newVals = []
3053	Found = False
3054	while S:
3055	if S[0] == '#':
3056	if Found:
3057	break
3058	if 'Bank' in S:
3059	if bank == int(S.split(':')[0].split()[1]):
3060	S = File.readline()
3061	continue
3062	else:
3063	S = File.readline()
3064	while S and '#Bank' not in S:
3065	S = File.readline()
3066	continue
3067	else: #a non #Bank file
3068	S = File.readline()
3069	continue
3070	Found = True
3071	[item,val] = S[:-1].split(':')
3072	newItems.append(item)
3073	try:
3074	newVals.append(float(val))
3075	except ValueError:
3076	newVals.append(val)
3077	S = File.readline()
3078	File.close()
3079	LoadG2fil()
3080	self.data['Instrument Parameters'][0] = G2fil.makeInstDict(newItems,newVals,len(newVals)*[False,])
3081
3082
3083	class G2Phase(G2ObjectWrapper):
3084	"""A wrapper object around a given phase.
3085
3086	Author: Jackson O'Donnell (jacksonhodonnell .at. gmail.com)
3087	"""
3088	def __init__(self, data, name, proj):
3089	self.data = data
3090	self.name = name
3091	self.proj = proj
3092
3093	@staticmethod
3094	def is_valid_refinement_key(key):
3095	valid_keys = ["Cell", "Atoms", "LeBail"]
3096	return key in valid_keys
3097
3098	@staticmethod
3099	def is_valid_HAP_refinement_key(key):
3100	valid_keys = ["Babinet", "Extinction", "HStrain", "Mustrain",
3101	"Pref.Ori.", "Show", "Size", "Use", "Scale"]
3102	return key in valid_keys
3103
3104	def atom(self, atomlabel):
3105	"""Returns the atom specified by atomlabel, or None if it does not
3106	exist.
3107
3108	:param str atomlabel: The name of the atom (e.g. "O2")
3109	:returns: A :class:`G2AtomRecord` object
3110	representing the atom.
3111	"""
3112	# Consult GSASIIobj.py for the meaning of this
3113	cx, ct, cs, cia = self.data['General']['AtomPtrs']
3114	ptrs = [cx, ct, cs, cia]
3115	atoms = self.data['Atoms']
3116	for atom in atoms:
3117	if atom[ct-1] == atomlabel:
3118	return G2AtomRecord(atom, ptrs, self.proj)
3119
3120	def atoms(self):
3121	"""Returns a list of atoms present in the current phase.
3122
3123	:returns: A list of :class:`G2AtomRecord` objects.
3124
3125	.. seealso::
3126	:meth:`~G2Phase.atom`
3127	:class:`G2AtomRecord`
3128	"""
3129	ptrs = self.data['General']['AtomPtrs']
3130	output = []
3131	atoms = self.data['Atoms']
3132	for atom in atoms:
3133	output.append(G2AtomRecord(atom, ptrs, self.proj))
3134	return output
3135
3136	def histograms(self):
3137	'''Returns a list of histogram names associated with the current phase.
3138	'''
3139	output = []
3140	for hname in self.data.get('Histograms', {}).keys():
3141	output.append(self.proj.histogram(hname))
3142	return output
3143
3144	@property
3145	def ranId(self):
3146	return self.data['ranId']
3147
3148	@property
3149	def id(self):
3150	return self.data['pId']
3151
3152	@id.setter
3153	def id(self, val):
3154	self.data['pId'] = val
3155
3156	def get_cell(self):
3157	"""Returns a dictionary of the cell parameters, with keys:
3158	'length_a', 'length_b', 'length_c', 'angle_alpha', 'angle_beta', 'angle_gamma', 'volume'
3159
3160	:returns: a dict
3161
3162	.. seealso::
3163	:meth:`~G2Phase.get_cell_and_esd`
3164
3165	"""
3166	cell = self.data['General']['Cell']
3167	return {'length_a': cell[1], 'length_b': cell[2], 'length_c': cell[3],
3168	'angle_alpha': cell[4], 'angle_beta': cell[5], 'angle_gamma': cell[6],
3169	'volume': cell[7]}
3170
3171	def get_cell_and_esd(self):
3172	"""
3173	Returns a pair of dictionaries, the first representing the unit cell, the second
3174	representing the estimated standard deviations of the unit cell.
3175
3176	:returns: a tuple of two dictionaries
3177
3178	.. seealso::
3179	:meth:`~G2Phase.get_cell`
3180
3181	"""
3182	# translated from GSASIIstrIO.ExportBaseclass.GetCell
3183	import GSASIIlattice as G2lat
3184	import GSASIImapvars as G2mv
3185	try:
3186	pfx = str(self.id) + '::'
3187	sgdata = self['General']['SGData']
3188	covDict = self.proj['Covariance']['data']
3189
3190	parmDict = dict(zip(covDict.get('varyList',[]),
3191	covDict.get('variables',[])))
3192	sigDict = dict(zip(covDict.get('varyList',[]),
3193	covDict.get('sig',[])))
3194
3195	if covDict.get('covMatrix') is not None:
3196	sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],
3197	covDict['varyList'],
3198	parmDict))
3199
3200	A, sigA = G2strIO.cellFill(pfx, sgdata, parmDict, sigDict)
3201	cellSig = G2strIO.getCellEsd(pfx, sgdata, A, self.proj['Covariance']['data'])
3202	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
3203	cellDict, cellSigDict = {}, {}
3204	for i, key in enumerate(['length_a', 'length_b', 'length_c',
3205	'angle_alpha', 'angle_beta', 'angle_gamma',
3206	'volume']):
3207	cellDict[key] = cellList[i]
3208	cellSigDict[key] = cellSig[i]
3209	return cellDict, cellSigDict
3210	except KeyError:
3211	cell = self.get_cell()
3212	return cell, {key: 0.0 for key in cell}
3213
3214	def export_CIF(self, outputname, quickmode=True):
3215	"""Write this phase to a .cif file named outputname
3216
3217	:param str outputname: The name of the .cif file to write to
3218	:param bool quickmode: Currently ignored. Carryover from exports.G2export_CIF"""
3219	# This code is all taken from exports/G2export_CIF.py
3220	# Functions copied have the same names
3221	import GSASIImath as G2mth
3222	import GSASIImapvars as G2mv
3223	from exports import G2export_CIF as cif
3224
3225	CIFdate = dt.datetime.strftime(dt.datetime.now(),"%Y-%m-%dT%H:%M")
3226	CIFname = os.path.splitext(self.proj.filename)[0]
3227	CIFname = os.path.split(CIFname)[1]
3228	CIFname = ''.join([c if ord(c) < 128 else ''
3229	for c in CIFname.replace(' ', '_')])
3230	try:
3231	author = self.proj['Controls']['data'].get('Author','').strip()
3232	except KeyError:
3233	pass
3234	oneblock = True
3235
3236	covDict = self.proj['Covariance']['data']
3237	parmDict = dict(zip(covDict.get('varyList',[]),
3238	covDict.get('variables',[])))
3239	sigDict = dict(zip(covDict.get('varyList',[]),
3240	covDict.get('sig',[])))
3241
3242	if covDict.get('covMatrix') is not None:
3243	sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],
3244	covDict['varyList'],
3245	parmDict))
3246
3247	with open(outputname, 'w') as fp:
3248	fp.write(' \n' + 70*'#' + '\n')
3249	cif.WriteCIFitem(fp, 'data_' + CIFname)
3250	# from exports.G2export_CIF.WritePhaseInfo
3251	cif.WriteCIFitem(fp, '\n# phase info for '+str(self.name) + ' follows')
3252	cif.WriteCIFitem(fp, '_pd_phase_name', self.name)
3253	# TODO get esds
3254	cellDict = self.get_cell()
3255	defsigL = 3[-0.00001] + 3[-0.001] + [-0.01] # significance to use when no sigma
3256	names = ['length_a','length_b','length_c',
3257	'angle_alpha','angle_beta ','angle_gamma',
3258	'volume']
3259	for key, val in cellDict.items():
3260	cif.WriteCIFitem(fp, '_cell_' + key, G2mth.ValEsd(val))
3261
3262	cif.WriteCIFitem(fp, '_symmetry_cell_setting',
3263	self.data['General']['SGData']['SGSys'])
3264
3265	spacegroup = self.data['General']['SGData']['SpGrp'].strip()
3266	# regularize capitalization and remove trailing H/R
3267	spacegroup = spacegroup[0].upper() + spacegroup[1:].lower().rstrip('rh ')
3268	cif.WriteCIFitem(fp, '_symmetry_space_group_name_H-M', spacegroup)
3269
3270	# generate symmetry operations including centering and center of symmetry
3271	SymOpList, offsetList, symOpList, G2oprList, G2opcodes = G2spc.AllOps(
3272	self.data['General']['SGData'])
3273	cif.WriteCIFitem(fp, 'loop_\n _space_group_symop_id\n _space_group_symop_operation_xyz')
3274	for i, op in enumerate(SymOpList,start=1):
3275	cif.WriteCIFitem(fp, ' {:3d} {:}'.format(i,op.lower()))
3276
3277	# TODO skipped histograms, exports/G2export_CIF.py:880
3278
3279	# report atom params
3280	if self.data['General']['Type'] in ['nuclear','macromolecular']: #this needs macromolecular variant, etc!
3281	cif.WriteAtomsNuclear(fp, self.data, self.name, parmDict, sigDict, [])
3282	# self._WriteAtomsNuclear(fp, parmDict, sigDict)
3283	else:
3284	raise G2ScriptException("no export for "+str(self.data['General']['Type'])+" coordinates implemented")
3285	# report cell contents
3286	cif.WriteComposition(fp, self.data, self.name, parmDict)
3287	if not quickmode and self.data['General']['Type'] == 'nuclear': # report distances and angles
3288	# WriteDistances(fp,self.name,SymOpList,offsetList,symOpList,G2oprList)
3289	raise NotImplementedError("only quickmode currently supported")
3290	if 'Map' in self.data['General'] and 'minmax' in self.data['General']['Map']:
3291	cif.WriteCIFitem(fp,'\n# Difference density results')
3292	MinMax = self.data['General']['Map']['minmax']
3293	cif.WriteCIFitem(fp,'_refine_diff_density_max',G2mth.ValEsd(MinMax[0],-0.009))
3294	cif.WriteCIFitem(fp,'_refine_diff_density_min',G2mth.ValEsd(MinMax[1],-0.009))
3295
3296
3297	def set_refinements(self, refs):
3298	"""Sets the phase refinement parameter 'key' to the specification 'value'
3299
3300	:param dict refs: A dictionary of the parameters to be set. See the
3301	:ref:`Phase_parameters_table` table for a description of
3302	this dictionary.
3303
3304	:returns: None"""
3305	for key, value in refs.items():
3306	if key == "Cell":
3307	self.data['General']['Cell'][0] = value
3308
3309	elif key == "Atoms":
3310	for atomlabel, atomrefinement in value.items():
3311	if atomlabel == 'all':
3312	for atom in self.atoms():
3313	atom.refinement_flags = atomrefinement
3314	else:
3315	atom = self.atom(atomlabel)
3316	if atom is None:
3317	raise ValueError("No such atom: " + atomlabel)
3318	atom.refinement_flags = atomrefinement
3319
3320	elif key == "LeBail":
3321	hists = self.data['Histograms']
3322	for hname, hoptions in hists.items():
3323	if 'LeBail' not in hoptions:
3324	hoptions['newLeBail'] = bool(True)
3325	hoptions['LeBail'] = bool(value)
3326	else:
3327	raise ValueError("Unknown key:", key)
3328
3329	def clear_refinements(self, refs):
3330	"""Clears a given set of parameters.
3331
3332	:param dict refs: The parameters to clear.
3333	See the :ref:`Phase_parameters_table` table for what can be specified.
3334	"""
3335	for key, value in refs.items():
3336	if key == "Cell":
3337	self.data['General']['Cell'][0] = False
3338	elif key == "Atoms":
3339	cx, ct, cs, cia = self.data['General']['AtomPtrs']
3340
3341	for atomlabel in value:
3342	atom = self.atom(atomlabel)
3343	# Set refinement to none
3344	atom.refinement_flags = ' '
3345	elif key == "LeBail":
3346	hists = self.data['Histograms']
3347	for hname, hoptions in hists.items():
3348	if 'LeBail' not in hoptions:
3349	hoptions['newLeBail'] = True
3350	hoptions['LeBail'] = False
3351	else:
3352	raise ValueError("Unknown key:", key)
3353
3354	def set_HAP_refinements(self, refs, histograms='all'):
3355	"""Sets the given HAP refinement parameters between this phase and
3356	the given histograms.
3357
3358	:param dict refs: A dictionary of the parameters to be set. See
3359	the :ref:`HAP_parameters_table` table for a description of this
3360	dictionary.
3361	:param histograms: Either 'all' (default) or a list of the histograms
3362	whose HAP parameters will be set with this phase. Histogram and phase
3363	must already be associated
3364
3365	:returns: None
3366	"""
3367	if not self.data['Histograms']:
3368	print("Error likely: Phase {} has no linked histograms".format(self.name))
3369	return
3370
3371	if histograms == 'all':
3372	histograms = self.data['Histograms'].values()
3373	else:
3374	histograms = [self.data['Histograms'][h.name] for h in histograms
3375	if h.name in self.data['Histograms']]
3376
3377	if not histograms:
3378	print("Skipping HAP set for phase {}, no selected histograms".format(self.name))
3379	return
3380	for key, val in refs.items():
3381	if key == 'Babinet':
3382	try:
3383	sets = list(val)
3384	except ValueError:
3385	sets = ['BabA', 'BabU']
3386	for param in sets:
3387	if param not in ['BabA', 'BabU']:
3388	raise ValueError("Not sure what to do with" + param)
3389	for h in histograms:
3390	h['Babinet'][param][1] = True
3391	elif key == 'Extinction':
3392	for h in histograms:
3393	h['Extinction'][1] = bool(val)
3394	elif key == 'HStrain':
3395	if isinstance(val,list) or isinstance(val,tuple):
3396	for h in histograms:
3397	if len(h['HStrain'][1]) != len(val):
3398	raise Exception('Need {} HStrain terms for phase {}'
3399	.format(len(h['HStrain'][1]),self.name))
3400	for i,v in enumerate(val):
3401	h['HStrain'][1][i] = bool(v)
3402	else:
3403	for h in histograms:
3404	h['HStrain'][1] = [bool(val) for p in h['HStrain'][1]]
3405	elif key == 'Mustrain':
3406	for h in histograms:
3407	mustrain = h['Mustrain']
3408	newType = None
3409	direction = None
3410	if isinstance(val, strtypes):
3411	if val in ['isotropic', 'uniaxial', 'generalized']:
3412	newType = val
3413	else:
3414	raise ValueError("Not a Mustrain type: " + val)
3415	elif isinstance(val, dict):
3416	newType = val.get('type', None)
3417	direction = val.get('direction', None)
3418
3419	if newType:
3420	mustrain[0] = newType
3421	if newType == 'isotropic':
3422	mustrain[2][0] = True == val.get('refine',False)
3423	mustrain[5] = [False for p in mustrain[4]]
3424	elif newType == 'uniaxial':
3425	if 'refine' in val:
3426	mustrain[2][0] = False
3427	types = val['refine']
3428	if isinstance(types, strtypes):
3429	types = [types]
3430	elif isinstance(types, bool):
3431	mustrain[2][1] = types
3432	mustrain[2][2] = types
3433	types = []
3434	else:
3435	raise ValueError("Not sure what to do with: "
3436	+ str(types))
3437	else:
3438	types = []
3439
3440	for unitype in types:
3441	if unitype == 'equatorial':
3442	mustrain[2][0] = True
3443	elif unitype == 'axial':
3444	mustrain[2][1] = True
3445	else:
3446	msg = 'Invalid uniaxial mustrain type'
3447	raise ValueError(msg + ': ' + unitype)
3448	else: # newtype == 'generalized'
3449	mustrain[2] = [False for p in mustrain[1]]
3450	if 'refine' in val:
3451	mustrain[5] = [True == val['refine']]*len(mustrain[5])
3452
3453	if direction:
3454	if len(direction) != 3:
3455	raise ValueError("Expected hkl, found", direction)
3456	direction = [int(n) for n in direction]
3457	mustrain[3] = direction
3458	elif key == 'Size':
3459	newSize = None
3460	if 'value' in val:
3461	newSize = float(val['value'])
3462	for h in histograms:
3463	size = h['Size']
3464	newType = None
3465	direction = None
3466	if isinstance(val, strtypes):
3467	if val in ['isotropic', 'uniaxial', 'ellipsoidal']:
3468	newType = val
3469	else:
3470	raise ValueError("Not a valid Size type: " + val)
3471	elif isinstance(val, dict):
3472	newType = val.get('type', None)
3473	direction = val.get('direction', None)
3474
3475	if newType:
3476	size[0] = newType
3477	refine = True == val.get('refine')
3478	if newType == 'isotropic' and refine is not None:
3479	size[2][0] = bool(refine)
3480	if newSize: size[1][0] = newSize
3481	elif newType == 'uniaxial' and refine is not None:
3482	size[2][1] = bool(refine)
3483	size[2][2] = bool(refine)
3484	if newSize: size[1][1] = size[1][2] =newSize
3485	elif newType == 'ellipsoidal' and refine is not None:
3486	size[5] = [bool(refine) for p in size[5]]
3487	if newSize: size[4] = [newSize for p in size[4]]
3488
3489	if direction:
3490	if len(direction) != 3:
3491	raise ValueError("Expected hkl, found", direction)
3492	direction = [int(n) for n in direction]
3493	size[3] = direction
3494	elif key == 'Pref.Ori.':
3495	for h in histograms:
3496	h['Pref.Ori.'][2] = bool(val)
3497	elif key == 'Show':
3498	for h in histograms:
3499	h['Show'] = bool(val)
3500	elif key == 'Use':
3501	for h in histograms:
3502	h['Use'] = bool(val)
3503	elif key == 'Scale':
3504	for h in histograms:
3505	h['Scale'][1] = bool(val)
3506	else:
3507	print(u'Unknown HAP key: '+key)
3508
3509	def _decodeHist(self,hist):
3510	'''Convert a histogram reference to a histogram name string
3511	'''
3512	if isinstance(hist, G2PwdrData):
3513	return hist.name
3514	elif hist in self.data['Histograms']:
3515	return hist
3516	elif type(hist) is int:
3517	return self.proj.histograms()[hist].name
3518	else:
3519	raise G2ScriptException("Invalid histogram reference: "+str(hist))
3520
3521	def getHAPvalues(self, histname):
3522	"""Returns a dict with HAP values for the selected histogram
3523
3524	:param histogram: is a histogram object (:class:`G2PwdrData`) or
3525	a histogram name or the index number of the histogram
3526
3527	:returns: HAP value dict
3528	"""
3529	return self.data['Histograms'][self._decodeHist(histname)]
3530
3531	def copyHAPvalues(self, sourcehist, targethistlist, skip=[]):
3532	"""Returns a dict with HAP values for the selected histogram
3533
3534	:param sourcehist: is a histogram object (:class:`G2PwdrData`) or
3535	a histogram name or the index number of the histogram
3536	:param list targethistlist: a list of histograms where each item in the
3537	list can be a histogram object (:class:`G2PwdrData`),
3538	a histogram name or the index number of the histogram.
3539	if the string 'all', then all histograms in the phase are used.
3540	:param list skip: items in the HAP dict that should not be
3541	copied. The default is an empty list, which causes all items
3542	to be copied. To see a list of items in the dict, use
3543	:meth:`getHAPvalues` or use an invalid item, such as '?'.
3544	"""
3545	sourcehist = self._decodeHist(sourcehist)
3546	if targethistlist == 'all':
3547	targethistlist = list(self.data['Histograms'].keys())
3548
3549	copydict = copy.deepcopy(self.data['Histograms'][sourcehist])
3550	for item in skip:
3551	if item in copydict:
3552	del copydict[item]
3553	else:
3554	print('items in HAP dict are: {}'.format(
3555	list(self.data['Histograms'][sourcehist])))
3556	raise Exception('HAP dict entry {} invalid'.format(item))
3557	for h in targethistlist:
3558	h = self._decodeHist(h)
3559	self.data['Histograms'][h].update(copydict)
3560
3561	#GSASIIpath.IPyBreak_base()
3562
3563	def clear_HAP_refinements(self, refs, histograms='all'):
3564	"""Clears the given HAP refinement parameters between this phase and
3565	the given histograms.
3566
3567	:param dict refs: A dictionary of the parameters to be cleared.
3568	See the the :ref:`HAP_parameters_table` table for what can be specified.
3569	:param histograms: Either 'all' (default) or a list of the histograms
3570	whose HAP parameters will be cleared with this phase. Histogram and
3571	phase must already be associated
3572
3573	:returns: None
3574	"""
3575	if histograms == 'all':
3576	histograms = self.data['Histograms'].values()
3577	else:
3578	histograms = [self.data['Histograms'][h.name] for h in histograms
3579	if h.name in self.data['Histograms']]
3580
3581	for key, val in refs.items():
3582	for h in histograms:
3583	if key == 'Babinet':
3584	try:
3585	sets = list(val)
3586	except ValueError:
3587	sets = ['BabA', 'BabU']
3588	for param in sets:
3589	if param not in ['BabA', 'BabU']:
3590	raise ValueError("Not sure what to do with" + param)
3591	for hist in histograms:
3592	hist['Babinet'][param][1] = False
3593	elif key == 'Extinction':
3594	for h in histograms:
3595	h['Extinction'][1] = False
3596	elif key == 'HStrain':
3597	for h in histograms:
3598	h['HStrain'][1] = [False for p in h['HStrain'][1]]
3599	elif key == 'Mustrain':
3600	for h in histograms:
3601	mustrain = h['Mustrain']
3602	mustrain[2] = [False for p in mustrain[2]]
3603	mustrain[5] = [False for p in mustrain[4]]
3604	elif key == 'Pref.Ori.':
3605	for h in histograms:
3606	h['Pref.Ori.'][2] = False
3607	elif key == 'Show':
3608	for h in histograms:
3609	h['Show'] = False
3610	elif key == 'Size':
3611	for h in histograms:
3612	size = h['Size']
3613	size[2] = [False for p in size[2]]
3614	size[5] = [False for p in size[5]]
3615	elif key == 'Use':
3616	for h in histograms:
3617	h['Use'] = False
3618	elif key == 'Scale':
3619	for h in histograms:
3620	h['Scale'][1] = False
3621	else:
3622	print(u'Unknown HAP key: '+key)
3623
3624	class G2Image(G2ObjectWrapper):
3625	"""Wrapper for an IMG tree entry, containing an image and various metadata.
3626	Note that in a GSASIIscriptable script, instances of G2Image will be created by
3627	calls to :meth:`G2Project.add_image` or :meth:`G2Project.images`, not via calls
3628	to :meth:`G2Image.__init__`.
3629
3630	Example use of G2Image:
3631
3632	>>> gpx = G2sc.G2Project(filename='itest.gpx')
3633	>>> imlst = gpx.add_image(idata,fmthint="TIF")
3634	>>> imlst[0].loadControls('stdSettings.imctrl')
3635	>>> imlst[0].setCalibrant('Si SRM640c')
3636	>>> imlst[0].loadMasks('stdMasks.immask')
3637	>>> imlst[0].Recalibrate()
3638	>>> imlst[0].setControl('outAzimuths',3)
3639	>>> pwdrList = imlst[0].Integrate()
3640
3641
3642	Sample script using an image:
3643
3644	.. code-block:: python
3645
3646	import os,sys
3647	sys.path.insert(0,'/Users/toby/software/G2/GSASII')
3648	import GSASIIscriptable as G2sc
3649	datadir = "/tmp/V4343_IntegrationError/"
3650	PathWrap = lambda fil: os.path.join(datadir,fil)
3651
3652	gpx = G2sc.G2Project(filename=PathWrap('inttest.gpx'))
3653	imlst = gpx.add_image(PathWrap('Si_free_dc800_1-00000.tif'),fmthint="TIF")
3654	imlst[0].loadControls(PathWrap('Si_free_dc800_1-00000.imctrl'))
3655	pwdrList = imlst[0].Integrate()
3656	gpx.save()
3657
3658	"""
3659	# parameters in that can be accessed via setControl. This may need future attention
3660	ControlList = {
3661	'int': ['calibskip', 'pixLimit', 'edgemin', 'outChannels',
3662	'outAzimuths'],
3663	'float': ['cutoff', 'setdist', 'wavelength', 'Flat Bkg',
3664	'azmthOff', 'tilt', 'calibdmin', 'rotation',
3665	'distance', 'DetDepth'],
3666	'bool': ['setRings', 'setDefault', 'centerAzm', 'fullIntegrate',
3667	'DetDepthRef', 'showLines'],
3668	'str': ['SampleShape', 'binType', 'formatName', 'color',
3669	'type', ],
3670	'list': ['GonioAngles', 'IOtth', 'LRazimuth', 'Oblique', 'PolaVal',
3671	'SampleAbs', 'center', 'ellipses', 'linescan',
3672	'pixelSize', 'range', 'ring', 'rings', 'size', ],
3673	'dict': ['varyList'],
3674	}
3675	'''Defines the items known to exist in the Image Controls tree section
3676	and the item's data types. A few are not included here
3677	('background image', 'dark image', 'Gain map', and 'calibrant') because
3678	these items have special set routines,
3679	where references to entries are checked to make sure their values are
3680	correct.
3681	'''
3682
3683	def __init__(self, data, name, proj):
3684	self.data = data
3685	self.name = name
3686	self.proj = proj
3687
3688	def setControl(self,arg,value):
3689	'''Set an Image Controls parameter in the current image.
3690	If the parameter is not found an exception is raised.
3691
3692	:param str arg: the name of a parameter (dict entry) in the
3693	image. The parameter must be found in :data:`ControlList`
3694	or an exception is raised.
3695	:param value: the value to set the parameter. The value is
3696	cast as the appropriate type from :data:`ControlList`.
3697	'''
3698	for typ in self.ControlList:
3699	if arg in self.ControlList[typ]: break
3700	else:
3701	print('Allowed args:\n',[nam for nam,typ in self.findControl('')])
3702	raise Exception('arg {} not defined in G2Image.setControl'
3703	.format(arg))
3704	try:
3705	if typ == 'int':
3706	self.data['Image Controls'][arg] = int(value)
3707	elif typ == 'float':
3708	self.data['Image Controls'][arg] = float(value)
3709	elif typ == 'bool':
3710	self.data['Image Controls'][arg] = bool(value)
3711	elif typ == 'str':
3712	self.data['Image Controls'][arg] = str(value)
3713	elif typ == 'list':
3714	self.data['Image Controls'][arg] = list(value)
3715	elif typ == 'dict':
3716	self.data['Image Controls'][arg] = dict(value)
3717	else:
3718	raise Exception('Unknown type {} for arg {} in G2Image.setControl'
3719	.format(typ,arg))
3720	except:
3721	raise Exception('Error formatting value {} as type {} for arg {} in G2Image.setControl'
3722	.format(value,typ,arg))
3723
3724	def getControl(self,arg):
3725	'''Return an Image Controls parameter in the current image.
3726	If the parameter is not found an exception is raised.
3727
3728	:param str arg: the name of a parameter (dict entry) in the
3729	image.
3730	:returns: the value as a int, float, list,...
3731	'''
3732	if arg in self.data['Image Controls']:
3733	return self.data['Image Controls'][arg]
3734	print(self.findControl(''))
3735	raise Exception('arg {} not defined in G2Image.getControl'.format(arg))
3736
3737	def findControl(self,arg=''):
3738	'''Finds the Image Controls parameter(s) in the current image
3739	that match the string in arg. Default is '' which returns all
3740	parameters.
3741
3742	Example:
3743
3744	>>> findControl('calib')
3745	[['calibskip', 'int'], ['calibdmin', 'float'], ['calibrant', 'str']]
3746
3747	:param str arg: a string containing part of the name of a
3748	parameter (dict entry) in the image's Image Controls.
3749	:returns: a list of matching entries in form
3750	[['item','type'], ['item','type'],...] where each 'item' string
3751	contains the sting in arg.
3752	'''
3753	matchList = []
3754	for typ in self.ControlList:
3755	for item in self.ControlList[typ]:
3756	if arg in item:
3757	matchList.append([item,typ])
3758	return matchList
3759
3760	def setCalibrant(self,calib):
3761	'''Set a calibrant for the current image
3762
3763	:param str calib: specifies a calibrant name which must be one of
3764	the entries in file ImageCalibrants.py. This is validated and
3765	an error provides a list of valid choices.
3766	'''
3767	import ImageCalibrants as calFile
3768	if calib in calFile.Calibrants.keys():
3769	self.data['Image Controls']['calibrant'] = calib
3770	return
3771	print('Calibrant {} is not valid. Valid calibrants'.format(calib))
3772	for i in calFile.Calibrants.keys():
3773	if i: print('\t"{}"'.format(i))
3774
3775	def setControlFile(self,typ,imageRef,mult=None):
3776	'''Set a image to be used as a background/dark/gain map image
3777
3778	:param str typ: specifies image type, which must be one of:
3779	'background image', 'dark image', 'gain map'; N.B. only the first
3780	four characters must be specified and case is ignored.
3781	:param imageRef: A reference to the desired image. Either the Image
3782	tree name (str), the image's index (int) or
3783	a image object (:class:`G2Image`)
3784	:param float mult: a multiplier to be applied to the image (not used
3785	for 'Gain map'; required for 'background image', 'dark image'
3786	'''
3787	if 'back' in typ.lower():
3788	key = 'background image'
3789	mult = float(mult)
3790	elif 'dark' in typ.lower():
3791	key = 'dark image'
3792	mult = float(mult)
3793	elif 'gain' in typ.lower():
3794	#key = 'Gain map'
3795	if mult is not None:
3796	print('Ignoring multiplier for Gain map')
3797	mult = None
3798	else:
3799	raise Exception("Invalid typ {} for setControlFile".format(typ))
3800	imgNam = self.proj.image(imageRef).name
3801	if mult is None:
3802	self.data['Image Controls']['Gain map'] = imgNam
3803	else:
3804	self.data['Image Controls'][key] = [imgNam,mult]
3805
3806	def loadControls(self,filename=None,imgDict=None):
3807	'''load controls from a .imctrl file
3808
3809	:param str filename: specifies a file to be read, which should end
3810	with .imctrl (defaults to None, meaning parameters are input
3811	with imgDict.)
3812	:param dict imgDict: contains a set of image parameters (defaults to
3813	None, meaning parameters are input with filename.)
3814	'''
3815	if filename:
3816	File = open(filename,'r')
3817	Slines = File.readlines()
3818	File.close()
3819	G2fil.LoadControls(Slines,self.data['Image Controls'])
3820	print('file {} read into {}'.format(filename,self.name))
3821	elif imgDict:
3822	self.data['Image Controls'].update(imgDict)
3823	print('Image controls set')
3824	else:
3825	raise Exception("loadControls called without imgDict or filename specified")
3826
3827	def saveControls(self,filename):
3828	'''write current controls values to a .imctrl file
3829
3830	:param str filename: specifies a file to write, which should end
3831	with .imctrl
3832	'''
3833	G2fil.WriteControls(filename,self.data['Image Controls'])
3834	print('file {} written from {}'.format(filename,self.name))
3835
3836	def loadMasks(self,filename,ignoreThreshold=False):
3837	'''load masks from a .immask file
3838
3839	:param str filename: specifies a file to be read, which should end
3840	with .immask
3841	:param bool ignoreThreshold: If True, masks are loaded with
3842	threshold masks. Default is False which means any Thresholds
3843	in the file are ignored.
3844	'''
3845	G2fil.readMasks(filename,self.data['Masks'],ignoreThreshold)
3846	print('file {} read into {}'.format(filename,self.name))
3847
3848	def getVary(self,*args):
3849	'''Return the refinement flag(s) for Image Controls parameter(s)
3850	in the current image.
3851	If the parameter is not found, an exception is raised.
3852
3853	:param str arg: the name of a refinement parameter in the
3854	varyList for the image. The name should be one of
3855	'dep', 'det-X', 'det-Y', 'dist', 'phi', 'tilt', or 'wave'
3856	:param str arg1: the name of a parameter (dict entry) as before,
3857	optional
3858
3859
3860	:returns: a list of bool value(s)
3861	'''
3862	res = []
3863	for arg in args:
3864	if arg in self.data['Image Controls']['varyList']:
3865	res.append(self.data['Image Controls']['varyList'][arg])
3866	else:
3867	raise Exception('arg {} not defined in G2Image.getVary'.format(arg))
3868	return res
3869
3870	def setVary(self,arg,value):
3871	'''Set a refinement flag for Image Controls parameter in the
3872	current image.
3873	If the parameter is not found an exception is raised.
3874
3875	:param str arg: the name of a refinement parameter in the
3876	varyList for the image. The name should be one of
3877	'dep', 'det-X', 'det-Y', 'dist', 'phi', 'tilt', or 'wave'
3878	:param str arg: the name of a parameter (dict entry) in the
3879	image. The parameter must be found in :data:`ControlList`
3880	or an exception is raised.
3881	:param value: the value to set the parameter. The value is
3882	cast as the appropriate type from :data:`ControlList`.
3883	'''
3884	if arg in self.data['Image Controls']['varyList']:
3885	self.data['Image Controls']['varyList'][arg] = bool(value)
3886	else:
3887	raise Exception('arg {} not defined in G2Image.setVary'.format(arg))
3888
3889	def Recalibrate(self):
3890	'''Invokes a recalibration fit (same as Image Controls/Calibration/Recalibrate
3891	menu command). Note that for this to work properly, the calibration
3892	coefficients (center, wavelength, ditance & tilts) must be fairly close.
3893	This may produce a better result if run more than once.
3894	'''
3895	LoadG2fil()
3896	ImageZ = _getCorrImage(Readers['Image'],self.proj,self)
3897	G2img.ImageRecalibrate(None,ImageZ,self.data['Image Controls'],self.data['Masks'])
3898
3899	def Integrate(self,name=None):
3900	'''Invokes an image integration (same as Image Controls/Integration/Integrate
3901	menu command). All parameters will have previously been set with Image Controls
3902	so no input is needed here. Note that if integration is performed on an
3903	image more than once, histogram entries may be overwritten. Use the name
3904	parameter to prevent this if desired.
3905
3906	:param str name: base name for created histogram(s). If None (default),
3907	the histogram name is taken from the image name.
3908	:returns: a list of created histogram (:class:`G2PwdrData`) objects.
3909	'''
3910	blkSize = 256 #256 seems to be optimal; will break in polymask if >1024
3911	ImageZ = _getCorrImage(Readers['Image'],self.proj,self)
3912	# do integration
3913	ints,azms,Xvals,cancel = G2img.ImageIntegrate(ImageZ,self.data['Image Controls'],self.data['Masks'],blkSize=blkSize)
3914	# code from here on based on G2IO.SaveIntegration, but places results in the current
3915	# project rather than tree
3916	X = Xvals[:-1]
3917	N = len(X)
3918
3919	data = self.data['Image Controls']
3920	Comments = self.data['Comments']
3921	# make name from image, unless overridden
3922	if name:
3923	if not name.startswith(data['type']+' '):
3924	name = data['type']+' '+name
3925	else:
3926	name = self.name.replace('IMG ',data['type']+' ')
3927	if 'PWDR' in name:
3928	if 'target' in data:
3929	names = ['Type','Lam1','Lam2','I(L2)/I(L1)','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
3930	codes = [0 for i in range(14)]
3931	else:
3932	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
3933	codes = [0 for i in range(12)]
3934	elif 'SASD' in name:
3935	names = ['Type','Lam','Zero','Azimuth']
3936	codes = [0 for i in range(4)]
3937	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
3938	Xminmax = [X[0],X[-1]]
3939	Azms = []
3940	dazm = 0.
3941	if data['fullIntegrate'] and data['outAzimuths'] == 1:
3942	Azms = [45.0,] #a poor man's average?
3943	else:
3944	for i,azm in enumerate(azms[:-1]):
3945	if azm > 360. and azms[i+1] > 360.:
3946	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
3947	else:
3948	Azms.append(G2img.meanAzm(azm,azms[i+1]))
3949	dazm = np.min(np.abs(np.diff(azms)))/2.
3950	# pull out integration results and make histograms for each
3951	IntgOutList = []
3952	for i,azm in enumerate(azms[:-1]):
3953	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
3954	# MT dict to contain histogram
3955	HistDict = {}
3956	histItems = [Aname]
3957	Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer
3958	Sample['Gonio. radius'] = data['distance']
3959	Sample['Omega'] = data['GonioAngles'][0]
3960	Sample['Chi'] = data['GonioAngles'][1]
3961	Sample['Phi'] = data['GonioAngles'][2]
3962	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
3963	polariz = 0.99 #set default polarization for synchrotron radiation!
3964	for item in Comments:
3965	if 'polariz' in item:
3966	try:
3967	polariz = float(item.split('=')[1])
3968	except:
3969	polariz = 0.99
3970	for key in ('Temperature','Pressure','Time','FreePrm1','FreePrm2','FreePrm3','Omega',
3971	'Chi','Phi'):
3972	if key.lower() in item.lower():
3973	try:
3974	Sample[key] = float(item.split('=')[1])
3975	except:
3976	pass
3977	# if 'label_prm' in item.lower():
3978	# for num in ('1','2','3'):
3979	# if 'label_prm'+num in item.lower():
3980	# Controls['FreePrm'+num] = item.split('=')[1].strip()
3981	if 'PWDR' in Aname:
3982	if 'target' in data: #from lab x-ray 2D imaging data
3983	waves = {'CuKa':[1.54051,1.54433],'TiKa':[2.74841,2.75207],'CrKa':[2.28962,2.29351],
3984	'FeKa':[1.93597,1.93991],'CoKa':[1.78892,1.79278],'MoKa':[0.70926,0.713543],
3985	'AgKa':[0.559363,0.563775]}
3986	wave1,wave2 = waves[data['target']]
3987	parms = ['PXC',wave1,wave2,0.5,0.0,polariz,290.,-40.,30.,6.,-14.,0.0,0.0001,Azms[i]]
3988	else:
3989	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
3990	elif 'SASD' in Aname:
3991	Sample['Trans'] = data['SampleAbs'][0]
3992	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
3993	Y = ints[i]
3994	Ymin = np.min(Y)
3995	Ymax = np.max(Y)
3996	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
3997	section = 'Comments'
3998	histItems += [section]
3999	HistDict[section] = Comments
4000	section = 'Limits'
4001	histItems += [section]
4002	HistDict[section] = copy.deepcopy([tuple(Xminmax),Xminmax])
4003	if 'PWDR' in Aname:
4004	section = 'Background'
4005	histItems += [section]
4006	HistDict[section] = [['chebyschev',1,3,1.0,0.0,0.0],
4007	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}]
4008	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
4009	for item in inst[0]:
4010	inst[0][item] = list(inst[0][item])
4011	section = 'Instrument Parameters'
4012	histItems += [section]
4013	HistDict[section] = inst
4014	if 'PWDR' in Aname:
4015	section = 'Sample Parameters'
4016	histItems += [section]
4017	HistDict[section] = Sample
4018	section = 'Peak List'
4019	histItems += [section]
4020	HistDict[section] = {'sigDict':{},'peaks':[]}
4021	section = 'Index Peak List'
4022	histItems += [section]
4023	HistDict[section] = [[],[]]
4024	section = 'Unit Cells List'
4025	histItems += [section]
4026	HistDict[section] = []
4027	section = 'Reflection Lists'
4028	histItems += [section]
4029	HistDict[section] = {}
4030	# elif 'SASD' in Aname:
4031	# section = 'Substances'
4032	# histItems += [section]
4033	# HistDict[section] = G2pdG.SetDefaultSubstances() # this needs to be moved
4034	# section = 'Sample Parameters'
4035	# histItems += [section]
4036	# HistDict[section] = Sample
4037	# section = 'Models'
4038	# histItems += [section]
4039	# HistDict[section] = G2pdG.SetDefaultSASDModel() # this needs to be moved
4040	valuesdict = {
4041	'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize),'Offset':[0.0,0.0],'delOffset':0.02*Ymax,
4042	'refOffset':-0.1Ymax,'refDelt':0.1Ymax,'Yminmax':[Ymin,Ymax]}
4043	# if Aname is already in the project replace it
4044	for j in self.proj.names:
4045	if j[0] == Aname:
4046	print('Replacing "{}" in project'.format(Aname))
4047	break
4048	else:
4049	print('Adding "{}" to project'.format(Aname))
4050	self.proj.names.append([Aname]+
4051	[u'Comments',u'Limits',u'Background',u'Instrument Parameters',
4052	u'Sample Parameters', u'Peak List', u'Index Peak List',
4053	u'Unit Cells List', u'Reflection Lists'])
4054	HistDict['data'] = [valuesdict,
4055	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]]
4056	self.proj.data[Aname] = HistDict
4057	IntgOutList.append(self.proj.histogram(Aname))
4058	return IntgOutList
4059
4060	##########################
4061	# Command Line Interface #
4062	##########################
4063	# Each of these takes an argparse.Namespace object as their argument,
4064	# representing the parsed command-line arguments for the relevant subcommand.
4065	# The argument specification for each is in the subcommands dictionary (see
4066	# below)
4067
4068	commandhelp={}
4069	commandhelp["create"] = "creates a GSAS-II project, optionally adding histograms and/or phases"
4070	def create(args):
4071	"""Implements the create command-line subcommand. This creates a GSAS-II project, optionally adding histograms and/or phases::
4072
4073	usage: GSASIIscriptable.py create [-h] [-d HISTOGRAMS [HISTOGRAMS ...]]
4074	[-i IPARAMS [IPARAMS ...]]
4075	[-p PHASES [PHASES ...]]
4076	filename
4077
4078	positional arguments::
4079
4080	filename the project file to create. should end in .gpx
4081
4082	optional arguments::
4083
4084	-h, --help show this help message and exit
4085	-d HISTOGRAMS [HISTOGRAMS ...], --histograms HISTOGRAMS [HISTOGRAMS ...]
4086	list of datafiles to add as histograms
4087	-i IPARAMS [IPARAMS ...], --iparams IPARAMS [IPARAMS ...]
4088	instrument parameter file, must be one for every
4089	histogram
4090	-p PHASES [PHASES ...], --phases PHASES [PHASES ...]
4091	list of phases to add. phases are automatically
4092	associated with all histograms given.
4093
4094	"""
4095	proj = G2Project(gpxfile=args.filename)
4096
4097	hist_objs = []
4098	if args.histograms:
4099	for h,i in zip(args.histograms,args.iparams):
4100	print("Adding histogram from",h,"with instparm ",i)
4101	hist_objs.append(proj.add_powder_histogram(h, i))
4102
4103	if args.phases:
4104	for p in args.phases:
4105	print("Adding phase from",p)
4106	proj.add_phase(p, histograms=hist_objs)
4107	print('Linking phase(s) to histogram(s):')
4108	for h in hist_objs:
4109	print (' '+h.name)
4110
4111	proj.save()
4112
4113	commandhelp["add"] = "adds histograms and/or phases to GSAS-II project"
4114	def add(args):
4115	"""Implements the add command-line subcommand. This adds histograms and/or phases to GSAS-II project::
4116
4117	usage: GSASIIscriptable.py add [-h] [-d HISTOGRAMS [HISTOGRAMS ...]]
4118	[-i IPARAMS [IPARAMS ...]]
4119	[-hf HISTOGRAMFORMAT] [-p PHASES [PHASES ...]]
4120	[-pf PHASEFORMAT] [-l HISTLIST [HISTLIST ...]]
4121	filename
4122
4123
4124	positional arguments::
4125
4126	filename the project file to open. Should end in .gpx
4127
4128	optional arguments::
4129
4130	-h, --help show this help message and exit
4131	-d HISTOGRAMS [HISTOGRAMS ...], --histograms HISTOGRAMS [HISTOGRAMS ...]
4132	list of datafiles to add as histograms
4133	-i IPARAMS [IPARAMS ...], --iparams IPARAMS [IPARAMS ...]
4134	instrument parameter file, must be one for every
4135	histogram
4136	-hf HISTOGRAMFORMAT, --histogramformat HISTOGRAMFORMAT
4137	format hint for histogram import. Applies to all
4138	histograms
4139	-p PHASES [PHASES ...], --phases PHASES [PHASES ...]
4140	list of phases to add. phases are automatically
4141	associated with all histograms given.
4142	-pf PHASEFORMAT, --phaseformat PHASEFORMAT
4143	format hint for phase import. Applies to all phases.
4144	Example: -pf CIF
4145	-l HISTLIST [HISTLIST ...], --histlist HISTLIST [HISTLIST ...]
4146	list of histgram indices to associate with added
4147	phases. If not specified, phases are associated with
4148	all previously loaded histograms. Example: -l 2 3 4
4149
4150	"""
4151	proj = G2Project(args.filename)
4152
4153	if args.histograms:
4154	for h,i in zip(args.histograms,args.iparams):
4155	print("Adding histogram from",h,"with instparm ",i)
4156	proj.add_powder_histogram(h, i, fmthint=args.histogramformat)
4157
4158	if args.phases:
4159	if not args.histlist:
4160	histlist = proj.histograms()
4161	else:
4162	histlist = [proj.histogram(i) for i in args.histlist]
4163
4164	for p in args.phases:
4165	print("Adding phase from",p)
4166	proj.add_phase(p, histograms=histlist, fmthint=args.phaseformat)
4167
4168	if not args.histlist:
4169	print('Linking phase(s) to all histogram(s)')
4170	else:
4171	print('Linking phase(s) to histogram(s):')
4172	for h in histlist:
4173	print (' '+h.name)
4174
4175	proj.save()
4176
4177
4178	commandhelp["dump"] = "Shows the contents of a GSAS-II project"
4179	def dump(args):
4180	"""Implements the dump command-line subcommand, which shows the contents of a GSAS-II project::
4181
4182	usage: GSASIIscriptable.py dump [-h] [-d] [-p] [-r] files [files ...]
4183
4184	positional arguments::
4185
4186	files
4187
4188	optional arguments::
4189
4190	-h, --help show this help message and exit
4191	-d, --histograms list histograms in files, overrides --raw
4192	-p, --phases list phases in files, overrides --raw
4193	-r, --raw dump raw file contents, default
4194
4195	"""
4196	if not args.histograms and not args.phases:
4197	args.raw = True
4198	if args.raw:
4199	import IPython.lib.pretty as pretty
4200
4201	for fname in args.files:
4202	if args.raw:
4203	proj, nameList = LoadDictFromProjFile(fname)
4204	print("file:", fname)
4205	print("names:", nameList)
4206	for key, val in proj.items():
4207	print(key, ":")
4208	pretty.pprint(val)
4209	else:
4210	proj = G2Project(fname)
4211	if args.histograms:
4212	hists = proj.histograms()
4213	for h in hists:
4214	print(fname, "hist", h.id, h.name)
4215	if args.phases:
4216	phase_list = proj.phases()
4217	for p in phase_list:
4218	print(fname, "phase", p.id, p.name)
4219
4220
4221	commandhelp["browse"] = "Load a GSAS-II project and then open a IPython shell to browse it"
4222	def IPyBrowse(args):
4223	"""Load a .gpx file and then open a IPython shell to browse it::
4224
4225	usage: GSASIIscriptable.py browse [-h] files [files ...]
4226
4227	positional arguments::
4228
4229	files list of files to browse
4230
4231	optional arguments::
4232
4233	-h, --help show this help message and exit
4234
4235	"""
4236	for fname in args.files:
4237	proj, nameList = LoadDictFromProjFile(fname)
4238	msg = "\nfname {} loaded into proj (dict) with names in nameList".format(fname)
4239	GSASIIpath.IPyBreak_base(msg)
4240	break
4241
4242
4243	commandhelp["refine"] = '''
4244	Conducts refinements on GSAS-II projects according to a list of refinement
4245	steps in a JSON dict
4246	'''
4247	def refine(args):
4248	"""Implements the refine command-line subcommand:
4249	conducts refinements on GSAS-II projects according to a JSON refinement dict::
4250
4251	usage: GSASIIscriptable.py refine [-h] gpxfile [refinements]
4252
4253	positional arguments::
4254
4255	gpxfile the project file to refine
4256	refinements json file of refinements to apply. if not present refines file
4257	as-is
4258
4259	optional arguments::
4260
4261	-h, --help show this help message and exit
4262
4263	"""
4264	proj = G2Project(args.gpxfile)
4265	if args.refinements is None:
4266	proj.refine()
4267	else:
4268	import json
4269	with open(args.refinements) as refs:
4270	refs = json.load(refs)
4271	if type(refs) is not dict:
4272	raise G2ScriptException("Error: JSON object must be a dict.")
4273	if "code" in refs:
4274	print("executing code:\n\| ",'\n\| '.join(refs['code']))
4275	exec('\n'.join(refs['code']))
4276	proj.do_refinements(refs['refinements'])
4277
4278
4279	commandhelp["export"] = "Export phase as CIF"
4280	def export(args):
4281	"""Implements the export command-line subcommand: Exports phase as CIF::
4282
4283	usage: GSASIIscriptable.py export [-h] gpxfile phase exportfile
4284
4285	positional arguments::
4286
4287	gpxfile the project file from which to export
4288	phase identifier of phase to export
4289	exportfile the .cif file to export to
4290
4291	optional arguments::
4292
4293	-h, --help show this help message and exit
4294
4295	"""
4296	proj = G2Project(args.gpxfile)
4297	phase = proj.phase(args.phase)
4298	phase.export_CIF(args.exportfile)
4299
4300
4301	def _args_kwargs(args, *kwargs):
4302	return args, kwargs
4303
4304	# A dictionary of the name of each subcommand, and a tuple
4305	# of its associated function and a list of its arguments
4306	# The arguments are passed directly to the add_argument() method
4307	# of an argparse.ArgumentParser
4308
4309	subcommands = {"create":
4310	(create, [_args_kwargs('filename',
4311	help='the project file to create. should end in .gpx'),
4312
4313	_args_kwargs('-d', '--histograms',
4314	nargs='+',
4315	help='list of datafiles to add as histograms'),
4316
4317	_args_kwargs('-i', '--iparams',
4318	nargs='+',
4319	help='instrument parameter file, must be one'
4320	' for every histogram'
4321	),
4322
4323	_args_kwargs('-p', '--phases',
4324	nargs='+',
4325	help='list of phases to add. phases are '
4326	'automatically associated with all '
4327	'histograms given.')]),
4328	"add": (add, [_args_kwargs('filename',
4329	help='the project file to open. Should end in .gpx'),
4330
4331	_args_kwargs('-d', '--histograms',
4332	nargs='+',
4333	help='list of datafiles to add as histograms'),
4334
4335	_args_kwargs('-i', '--iparams',
4336	nargs='+',
4337	help='instrument parameter file, must be one'
4338	' for every histogram'
4339	),
4340
4341	_args_kwargs('-hf', '--histogramformat',
4342	help='format hint for histogram import. Applies to all'
4343	' histograms'
4344	),
4345
4346	_args_kwargs('-p', '--phases',
4347	nargs='+',
4348	help='list of phases to add. phases are '
4349	'automatically associated with all '
4350	'histograms given.'),
4351
4352	_args_kwargs('-pf', '--phaseformat',
4353	help='format hint for phase import. Applies to all'
4354	' phases. Example: -pf CIF'
4355	),
4356
4357	_args_kwargs('-l', '--histlist',
4358	nargs='+',
4359	help='list of histgram indices to associate with added'
4360	' phases. If not specified, phases are'
4361	' associated with all previously loaded'
4362	' histograms. Example: -l 2 3 4')]),
4363
4364	"dump": (dump, [_args_kwargs('-d', '--histograms',
4365	action='store_true',
4366	help='list histograms in files, overrides --raw'),
4367
4368	_args_kwargs('-p', '--phases',
4369	action='store_true',
4370	help='list phases in files, overrides --raw'),
4371
4372	_args_kwargs('-r', '--raw',
4373	action='store_true', help='dump raw file contents, default'),
4374
4375	_args_kwargs('files', nargs='+')]),
4376
4377	"refine":
4378	(refine, [_args_kwargs('gpxfile', help='the project file to refine'),
4379	_args_kwargs('refinements',
4380	help='JSON file of refinements to apply. if not present'
4381	' refines file as-is',
4382	default=None,
4383	nargs='?')]),
4384
4385	"export": (export, [_args_kwargs('gpxfile',
4386	help='the project file from which to export'),
4387	_args_kwargs('phase', help='identifier of phase to export'),
4388	_args_kwargs('exportfile', help='the .cif file to export to')]),
4389	"browse": (IPyBrowse, [_args_kwargs('files', nargs='+',
4390	help='list of files to browse')])}
4391
4392
4393	def main():
4394	'''The command-line interface for calling GSASIIscriptable as a shell command,
4395	where it is expected to be called as::
4396
4397	python GSASIIscriptable.py <subcommand> <file.gpx> <options>
4398
4399	The following subcommands are defined:
4400
4401	* create, see :func:`create`
4402	* add, see :func:`add`
4403	* dump, see :func:`dump`
4404	* refine, see :func:`refine`
4405	* export, :func:`export`
4406	* browse, see :func:`IPyBrowse`
4407
4408	.. seealso::
4409	:func:`create`
4410	:func:`add`
4411	:func:`dump`
4412	:func:`refine`
4413	:func:`export`
4414	:func:`IPyBrowse`
4415	'''
4416	parser = argparse.ArgumentParser(description=
4417	"Use of "+os.path.split(__file__)[1]+" Allows GSAS-II actions from command line."
4418	)
4419	subs = parser.add_subparsers()
4420
4421	# Create all of the specified subparsers
4422	for name, (func, args) in subcommands.items():
4423	new_parser = subs.add_parser(name,help=commandhelp.get(name),
4424	description='Command "'+name+'" '+commandhelp.get(name))
4425	for listargs, kwds in args:
4426	new_parser.add_argument(listargs, *kwds)
4427	new_parser.set_defaults(func=func)
4428
4429	# Parse and trigger subcommand
4430	result = parser.parse_args()
4431	result.func(result)
4432
4433	if __name__ == '__main__':
4434	#fname='/tmp/corundum-template.gpx'
4435	#prj = G2Project(fname)
4436	main()

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