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Commit 190c510

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author
Joel Bernier
committed
bug fix in fitgrains, added cfg for skipping option
1 parent 892eba9 commit 190c510

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3 files changed

+80
-63
lines changed

3 files changed

+80
-63
lines changed

‎hexrd/config/fitgrains.py‎

Lines changed: 14 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -95,6 +95,20 @@ def refit(self):
9595
return temp
9696

9797

98+
"""
99+
PROBABLY JUST SCRAP THIS...s
100+
"""
101+
@property
102+
def skip_on_estimate(self):
103+
key = 'fit_grains:skip_on_estimate'
104+
temp = self._cfg.get(key, False)
105+
if temp in (True, False):
106+
return temp
107+
raise RuntimeError(
108+
'"%s" must be true or false, got "%s"' % (key, temp)
109+
)
110+
111+
98112
@property
99113
def fit_only(self):
100114
key = 'fit_grains:fit_only'

‎hexrd/fitgrains.py‎

Lines changed: 7 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,6 @@
3434

3535
logger = logging.getLogger(__name__)
3636

37-
3837
# grain parameter refinement flags
3938
gFlag = np.array([1, 1, 1,
4039
1, 1, 1,
@@ -475,9 +474,13 @@ def get_residuals(self, grain_params):
475474
def loop(self):
476475
id, grain_params = self._jobs.get(False)
477476

478-
# skips the first loop if have_estimate is True
479-
have_estimate = not np.all(grain_params[-9] == [0,0,0,1,1,1,0,0,0])
480-
iterations = (have_estimate, len(self._p['eta_tol']))
477+
# slated for removal ## skips the first loop if have_estimate is True
478+
# slated for removal #if self._p['skip_on_estimate']:
479+
# slated for removal # have_estimate = not np.all(grain_params[-9:] == [0,0,0,1,1,1,0,0,0])
480+
# slated for removal # iterations = (have_estimate, len(self._p['eta_tol']))
481+
# slated for removal #else:
482+
# slated for removal # iterations = (0, len(self._p['eta_tol']))
483+
iterations = (0, len(self._p['eta_tol']))
481484
for iteration in range(*iterations):
482485
# pull spots if asked to, otherwise just fit
483486
if not self._p['fit_only']:

‎hexrd/xrd/xrdutil.py‎

Lines changed: 59 additions & 59 deletions
Original file line numberDiff line numberDiff line change
@@ -1718,82 +1718,82 @@ def __init__(self, ome_eta):
17181718
self.etas = ome_eta.etas
17191719
self.omegas = ome_eta.omegas
17201720
return
1721-
1721+
17221722

17231723

17241724
# not ready # class BaseEtaOme(object):
17251725
# not ready # """
1726-
# not ready # eta-ome map base class derived from new YAML config
1727-
# not ready #
1726+
# not ready # eta-ome map base class derived from new YAML config
1727+
# not ready #
17281728
# not ready # ...for now...
1729-
# not ready #
1729+
# not ready #
17301730
# not ready # must provide:
1731-
# not ready #
1731+
# not ready #
17321732
# not ready # self.dataStore
17331733
# not ready # self.planeData
1734-
# not ready # self.iHKLList
1735-
# not ready # self.etaEdges # IN RADIANS
1734+
# not ready # self.iHKLList
1735+
# not ready # self.etaEdges # IN RADIANS
17361736
# not ready # self.omeEdges # IN RADIANS
17371737
# not ready # self.etas # IN RADIANS
17381738
# not ready # self.omegas # IN RADIANS
1739-
# not ready #
1739+
# not ready #
17401740
# not ready # This wrapper will provide all but dataStore.
17411741
# not ready # """
17421742
# not ready # def __init__(self, cfg, reader=None, eta_step=None):
17431743
# not ready # """
1744-
# not ready # currently, reader has to be None *OLD* class type until fixed with new imageIO;
1744+
# not ready # currently, reader has to be None *OLD* class type until fixed with new imageIO;
17451745
# not ready # if None, then the frame_cache.npz specified by the config must exist
17461746
# not ready # """
17471747
# not ready # self.cfg = cfg
17481748
# not ready # self.instr_cfg = get_instrument_parameters(cfg)
1749-
# not ready #
1749+
# not ready #
17501750
# not ready # # currently hard-coded to do reader from npz frame cache
17511751
# not ready # # kwarg *MUST* be 'new' style reader
17521752
# not ready # if reader is None:
17531753
# not ready # self.__reader = get_frames(reader, self.cfg)
17541754
# not ready # else:
17551755
# not ready # self.__reader = reader
1756-
# not ready #
1756+
# not ready #
17571757
# not ready # # set eta_step IN DEGREES
17581758
# not ready # if eta_step is None:
17591759
# not ready # self._eta_step = self.cfg.image_series.omega.step
17601760
# not ready # else:
1761-
# not ready # self._eta_step = abs(eta_step) # just in case negative...
1762-
# not ready #
1761+
# not ready # self._eta_step = abs(eta_step) # just in case negative...
1762+
# not ready #
17631763
# not ready # material_list = cPickle.load(open(cfg.material.definitions, 'r'))
17641764
# not ready # material_names = [material_list[i].name for i in range(len(material_list))]
17651765
# not ready # material_dict = dict(zip(material_names, material_list))
17661766
# not ready # self.planeData = material_dict[cfg.material.active].planeData
1767-
# not ready #
1767+
# not ready #
17681768
# not ready # self._iHKLList = None
1769-
# not ready #
1769+
# not ready #
17701770
# not ready # self._etaEdges = None
17711771
# not ready # self._omeEdges = None
17721772
# not ready # self._etas = None
17731773
# not ready # self._omegas = None
1774-
# not ready #
1774+
# not ready #
17751775
# not ready # return
1776-
# not ready #
1776+
# not ready #
17771777
# not ready # @property
17781778
# not ready # def iHKLList(self):
17791779
# not ready # return self._iHKLList
17801780
# not ready # @iHKLList.getter
17811781
# not ready # def iHKLList(self, ids=None):
17821782
# not ready # """
1783-
# not ready # ids must be a list
1783+
# not ready # ids must be a list
17841784
# not ready # """
17851785
# not ready # if ids is not None:
17861786
# not ready # assert hasattr(ids, '__len__'), "ids must be a list or list-like object"
1787-
# not ready #
1788-
# not ready # # start with all available
1787+
# not ready #
1788+
# not ready # # start with all available
17891789
# not ready # active_hkls = range(pd.hkls.shape[1])
17901790
# not ready # # check cfg file
17911791
# not ready # temp = cfg.find_orientations.orientation_maps.active_hkls
17921792
# not ready # # override if spec'd explicitly in cfg
17931793
# not ready # active_hkls = active_hkls if temp == 'all' else temp
17941794
# not ready # # override with hkls from command line, if specified
17951795
# not ready # return ids if ids is not None else active_hkls
1796-
# not ready #
1796+
# not ready #
17971797
# not ready # @property
17981798
# not ready # def omegas(self):
17991799
# not ready # return self._omegas
@@ -1806,53 +1806,53 @@ def __init__(self, ome_eta):
18061806
# not ready # ome_start = self.__reader[1][0]
18071807
# not ready # ome_step = self.__reader[1][1]
18081808
# not ready # return ome_step*(num.arange(num_ome) + 0.5) + ome_start
1809-
# not ready #
1809+
# not ready #
18101810
# not ready # @property
18111811
# not ready # def eta_step(self):
18121812
# not ready # return self._eta_step
1813-
# not ready #
1813+
# not ready #
18141814
# not ready # @property
18151815
# not ready # def etas(self):
18161816
# not ready # return self._etas
18171817
# not ready # @etas.getter
18181818
# not ready # def etas(self):
18191819
# not ready # """
18201820
# not ready # range is forced to be [-180, 180] for now, so step must be positive
1821-
# not ready #
1821+
# not ready #
18221822
# not ready # step is same as omega unless specified (in degrees)
18231823
# not ready # """
18241824
# not ready # num_eta = int(360/float(abs(self.eta_step)))
18251825
# not ready # return num.radians(self.eta_step)*(num.arange(num_eta) + 0.5) - num.pi
1826-
# not ready #
1826+
# not ready #
18271827
# not ready # @property
18281828
# not ready # def omeEdges(self):
18291829
# not ready # return self._omeEdges
18301830
# not ready # @omeEdges.getter
18311831
# not ready # def omeEdges(self):
18321832
# not ready # ome_step = self.omegas[1] - self.omegas[0] # same as self.__reader[1][1]
18331833
# not ready # return num.hstack([self.omegas - 0.5*ome_step, self.omegas[-1] + 0.5*ome_step])
1834-
# not ready #
1834+
# not ready #
18351835
# not ready # @property
18361836
# not ready # def etaEdges(self):
18371837
# not ready # return self._etaEdges
18381838
# not ready # @etaEdges.getter
18391839
# not ready # def etaEdges(self):
18401840
# not ready # return num.hstack([self.etas - 0.5*eta_step, self.etas[-1] + 0.5*eta_step])
1841-
# not ready #
1841+
# not ready #
18421842
# not ready # class EtaOmeMaps(BaseEtaOme):
18431843
# not ready # """
18441844
# not ready # """
18451845
# not ready # def __init__(self, cfg, reader=None, eta_step=None,
1846-
# not ready # omega=0., tVec_s=num.zeros(3),
1846+
# not ready # omega=0., tVec_s=num.zeros(3),
18471847
# not ready # npdiv=2):
1848-
# not ready #
1848+
# not ready #
18491849
# not ready # # first init the base class
18501850
# not ready # super( EtaOmeMaps, self ).__init__(cfg, reader=reader, eta_step=eta_step)
1851-
# not ready #
1851+
# not ready #
18521852
# not ready # # grac relevant tolerances for patches
18531853
# not ready # tth_tol = num.degrees(self.planeData.tThWidth)
18541854
# not ready # eta_tol = num.degrees(abs(self.etas[1]-self.etas[0]))
1855-
# not ready #
1855+
# not ready #
18561856
# not ready # # grab distortion
18571857
# not ready # if instr_cfg['detector']['distortion']['function_name'] is None:
18581858
# not ready # distortion = None
@@ -1863,35 +1863,35 @@ def __init__(self, ome_eta):
18631863
# not ready # )
18641864
# not ready # # stack parameters
18651865
# not ready # detector_params = num.hstack([
1866-
# not ready # instr_cfg['detector']['transform']['tilt_angles'],
1866+
# not ready # instr_cfg['detector']['transform']['tilt_angles'],
18671867
# not ready # instr_cfg['detector']['transform']['t_vec_d'],
1868-
# not ready # instr_cfg['oscillation_stage']['chi'],
1869-
# not ready # instr_cfg['oscillation_stage']['t_vec_s'],
1868+
# not ready # instr_cfg['oscillation_stage']['chi'],
1869+
# not ready # instr_cfg['oscillation_stage']['t_vec_s'],
18701870
# not ready # ])
18711871
# not ready # pixel_pitch = instr_cfg['detector']['pixels']['size']
18721872
# not ready # chi = self.instr_cfg['oscillation_stage']['chi'] # in DEGREES
1873-
# not ready #
1873+
# not ready #
18741874
# not ready # # 6 detector affine xform parameters
18751875
# not ready # rMat_d = makeDetectorRotMat(detector_params[:3])
18761876
# not ready # tVec_d = detector_params[3:6]
1877-
# not ready #
1877+
# not ready #
18781878
# not ready # # 'dummy' sample frame rot mat
18791879
# not ready # rMats_s = makeOscillRotMat(num.radians([chi, omega]))
1880-
# not ready #
1880+
# not ready #
18811881
# not ready # # since making maps for all eta, must hand trivial crystal params
18821882
# not ready # rMat_c = np.eye(3)
18831883
# not ready # tVec_c = np.zeros(3)
1884-
# not ready #
1884+
# not ready #
18851885
# not ready # # make angle arrays for patches
18861886
# not ready # neta = len(self.etas)
18871887
# not ready # nome = len(reader[0])
1888-
# not ready #
1888+
# not ready #
18891889
# not ready # # make full angs list
18901890
# not ready # angs = [num.vstack([tth*num.ones(neta),
18911891
# not ready # etas,
18921892
# not ready # num.zeros(nome)])
18931893
# not ready # for tth in self.planeData.getTTh()]
1894-
# not ready #
1894+
# not ready #
18951895
# not ready # """SET MAPS CONTAINER AS ATTRIBUTE"""
18961896
# not ready # self.dataStore = num.zeros((len(angs), nome, neta))
18971897
# not ready # for i_ring in range(len(angs)):
@@ -1900,7 +1900,7 @@ def __init__(self, ome_eta):
19001900
# not ready # xydet_ring = xfcapi.gvecToDetectorXY(gVec_ring_l,
19011901
# not ready # rMat_d, rMat_s, rMat_c,
19021902
# not ready # tVec_d, tVec_s, tVec_c)
1903-
# not ready #
1903+
# not ready #
19041904
# not ready # if distortion is not None:
19051905
# not ready # det_xy = distortion[0](xydet_ring,
19061906
# not ready # distortion[1],
@@ -1909,15 +1909,15 @@ def __init__(self, ome_eta):
19091909
# not ready # rMat_d, rMat_s,
19101910
# not ready # tVec_d, tVec_s, tVec_c,
19111911
# not ready # distortion=distortion)
1912-
# not ready #
1912+
# not ready #
19131913
# not ready # patches = make_reflection_patches(self.instr_cfg,
19141914
# not ready # angs[i_ring].T[:, :2], ang_ps,
19151915
# not ready # omega=None,
19161916
# not ready # tth_tol=tth_tol, eta_tol=eta_tol,
19171917
# not ready # distortion=distortion,
19181918
# not ready # npdiv=npdiv, quiet=False,
19191919
# not ready # compute_areas_func=gutil.compute_areas)
1920-
# not ready #
1920+
# not ready #
19211921
# not ready # for i in range(nome):
19221922
# not ready # this_frame = num.array(reader[0][i].todense())
19231923
# not ready # for j in range(neta):
@@ -3464,14 +3464,14 @@ def simulateGVecs(pd, detector_params, grain_params,
34643464
# first find valid G-vectors
34653465
angList = num.vstack(xfcapi.oscillAnglesOfHKLs(full_hkls[:, 1:], chi, rMat_c, bMat, wlen, vInv=vInv_s))
34663466
allAngs, allHKLs = _filter_hkls_eta_ome(full_hkls, angList, eta_range, ome_range)
3467-
3467+
34683468
if len(allAngs) == 0:
34693469
valid_ids = []
3470-
valid_hkl = []
3471-
valid_ang = []
3472-
valid_xy = []
3470+
valid_hkl = []
3471+
valid_ang = []
3472+
valid_xy = []
34733473
ang_ps = []
3474-
else:
3474+
else:
34753475
#...preallocate for speed...?
34763476
det_xy, rMat_s = _project_on_detector_plane(allHKLs[:, 1:], allAngs, bMat,
34773477
rMat_d, rMat_c, chi,
@@ -3494,11 +3494,11 @@ def simulateGVecs(pd, detector_params, grain_params,
34943494

34953495

34963496
def simulateLauePattern(hkls, bMat,
3497-
rmat_d, tvec_d,
3498-
panel_dims, panel_buffer=5,
3497+
rmat_d, tvec_d,
3498+
panel_dims, panel_buffer=5,
34993499
minEnergy=8, maxEnergy=24,
35003500
rmat_s=num.eye(3),
3501-
grain_params=None,
3501+
grain_params=None,
35023502
distortion=None):
35033503

35043504
# parse energy ranges
@@ -3517,7 +3517,7 @@ def simulateLauePattern(hkls, bMat,
35173517
if grain_params is None:
35183518
grain_params = num.atleast_2d([0., 0., 0., 0., 0., 0., 1., 1., 1., 0., 0., 0.])
35193519
n_grains = len(grain_params)
3520-
3520+
35213521
# dummy translation vector... make input
35223522
tvec_s = num.zeros((3, 1))
35233523

@@ -3526,14 +3526,14 @@ def simulateLauePattern(hkls, bMat,
35263526

35273527
# unit G-vectors in crystal frame
35283528
ghat_c = mutil.unitVector(num.dot(bMat, hkls))
3529-
3529+
35303530
# pre-allocate output arrays
35313531
xy_det = num.nan*num.ones((n_grains, nhkls_tot, 2))
35323532
hkls_in = num.nan*num.ones((n_grains, 3, nhkls_tot))
35333533
angles = num.nan*num.ones((n_grains, nhkls_tot, 2))
35343534
dspacing = num.nan*num.ones((n_grains, nhkls_tot))
35353535
energy = num.nan*num.ones((n_grains, nhkls_tot))
3536-
3536+
35373537
"""
35383538
LOOP OVER GRAINS
35393539
"""
@@ -3564,20 +3564,20 @@ def simulateLauePattern(hkls, bMat,
35643564
tvec_d, tvec_s, tvec_c
35653565
)
35663566
tth_eta = num.vstack(tth_eta).T
3567-
3567+
35683568
# warp measured points
35693569
if distortion is not None:
35703570
if len(distortion) == 2:
35713571
dpts = distortion[0](dpts, distortion[1], invert=True)
3572-
3572+
35733573
# plane spacings and energies
35743574
dsp = 1. / mutil.columnNorm(num.dot(bMat, dhkl))
35753575
wlen = 2*dsp*num.sin(0.5*tth_eta[:, 0])
35763576

35773577
# find on spatial extent of detector
3578-
xTest = num.logical_and(dpts[0, :] >= -0.5*panel_dims[1] + panel_buffer,
3578+
xTest = num.logical_and(dpts[0, :] >= -0.5*panel_dims[1] + panel_buffer,
35793579
dpts[0, :] <= 0.5*panel_dims[1] - panel_buffer)
3580-
yTest = num.logical_and(dpts[1, :] >= -0.5*panel_dims[0] + panel_buffer,
3580+
yTest = num.logical_and(dpts[1, :] >= -0.5*panel_dims[0] + panel_buffer,
35813581
dpts[1, :] <= 0.5*panel_dims[0] - panel_buffer)
35823582

35833583
onDetector = num.logical_and(xTest, yTest)
@@ -3840,7 +3840,7 @@ def make_reflection_patches(instr_cfg, tth_eta, ang_pixel_size,
38403840
pass
38413841

38423842
areas = compute_areas_func(xy_eval_vtx, conn)
3843-
3843+
38443844
# EVALUATION POINTS
38453845
# * for lack of a better option will use centroids
38463846
tth_eta_cen = gutil.cellCentroids( num.atleast_2d(gVec_angs_vtx[:, :2]), conn )

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