diff --git a/fsrc/bld.bat b/ImageD11/depreciated/fsrc/bld.bat similarity index 100% rename from fsrc/bld.bat rename to ImageD11/depreciated/fsrc/bld.bat diff --git a/fsrc/cImageD11_wrap.pyx b/ImageD11/depreciated/fsrc/cImageD11_wrap.pyx similarity index 100% rename from fsrc/cImageD11_wrap.pyx rename to ImageD11/depreciated/fsrc/cImageD11_wrap.pyx diff --git a/fsrc/fImageD11.f90 b/ImageD11/depreciated/fsrc/fImageD11.f90 similarity index 100% rename from fsrc/fImageD11.f90 rename to ImageD11/depreciated/fsrc/fImageD11.f90 diff --git a/fsrc/fImageD11_testprog.f90 b/ImageD11/depreciated/fsrc/fImageD11_testprog.f90 similarity index 100% rename from fsrc/fImageD11_testprog.f90 rename to ImageD11/depreciated/fsrc/fImageD11_testprog.f90 diff --git a/fsrc/fImageD11module.c b/ImageD11/depreciated/fsrc/fImageD11module.c similarity index 100% rename from fsrc/fImageD11module.c rename to ImageD11/depreciated/fsrc/fImageD11module.c diff --git a/fsrc/setup.py b/ImageD11/depreciated/fsrc/setup.py similarity index 100% rename from fsrc/setup.py rename to ImageD11/depreciated/fsrc/setup.py diff --git a/src/test_cf.py b/ImageD11/depreciated/fsrc/test_cf.py similarity index 100% rename from src/test_cf.py rename to ImageD11/depreciated/fsrc/test_cf.py diff --git a/fsrc/test_xlylzl.py b/ImageD11/depreciated/fsrc/test_xlylzl.py similarity index 100% rename from fsrc/test_xlylzl.py rename to ImageD11/depreciated/fsrc/test_xlylzl.py diff --git a/fsrc/test_xlylzl_c.py b/ImageD11/depreciated/fsrc/test_xlylzl_c.py similarity index 100% rename from fsrc/test_xlylzl_c.py rename to ImageD11/depreciated/fsrc/test_xlylzl_c.py diff --git a/fsrc/tst.py b/ImageD11/depreciated/fsrc/tst.py similarity index 100% rename from fsrc/tst.py rename to ImageD11/depreciated/fsrc/tst.py diff --git a/src/test_f2py.py b/ImageD11/depreciated/test_f2py.py similarity index 100% rename from src/test_f2py.py rename to ImageD11/depreciated/test_f2py.py diff --git a/ImageD11/indexer.py b/ImageD11/indexer.py index 15edd02d..55e15d68 100644 --- a/ImageD11/indexer.py +++ b/ImageD11/indexer.py @@ -20,8 +20,7 @@ import numpy as np -from ImageD11 import closest, grain, transform, fImageD11, indexing -from . import unitcell +from ImageD11 import grain, transform, cImageD11, indexing, unitcell import scipy.optimize import math, time, sys, logging @@ -76,16 +75,16 @@ def updatecolfile(self): self.cf.addcolumn(xl,"xl") self.cf.addcolumn(yl,"yl") self.cf.addcolumn(zl,"zl") - self.peaks_xyz = np.array((self.cf.xl,self.cf.yl,self.cf.zl)) + self.peaks_xyzT = np.array(zip(self.cf.xl,self.cf.yl,self.cf.zl)) om = self.cf.omega - sign = self.transformpars.get("omegasign") + osign = self.transformpars.get("omegasign") tth, eta = transform.compute_tth_eta_from_xyz( - self.peaks_xyz, om*sign, + self.peaks_xyzT.T, om*osign, **self.transformpars.parameters) self.cf.addcolumn( tth, "tth", ) self.cf.addcolumn( eta, "eta", ) gx, gy, gz = transform.compute_g_vectors( - tth, eta, om*sign, + tth, eta, om*osign, wvln = self.transformpars.get("wavelength"), wedge = self.transformpars.get("wedge"), chi = self.transformpars.get("chi") ) @@ -207,10 +206,11 @@ def pairs(self, hkl1, hkl2, cos_tol = 0.02, hkl_tol = 0.1): ub = np.dot( U, self.unitcell.B) ubi = np.linalg.inv( ub ) ubio = ubi.copy() - npks = closest.score(ubi,gvf,hkl_tol) + npks = cImageD11.score(ubi,gvf,hkl_tol) pairs.append( (ind1[i], ind2[k], U, ubi ) ) print(npks, end=' ') - ubi, trans = self.refine( ubi, [0.,0.,0.], tol=hkl_tol ) + + ubi, trans = self.refine( ubi, np.zeros(3,np.float), tol=hkl_tol ) inds, hkls = self.assign( ubi, trans, hkl_tol ) ubi, trans = self.refine( ubi, trans, inds = inds, hkls= hkls, tol=hkl_tol ) print(npks, ubi) @@ -223,8 +223,8 @@ def pairs(self, hkl1, hkl2, cos_tol = 0.02, hkl_tol = 0.1): def assign(self, ubi, translation, tol): - gv = np.zeros(self.peaks_xyz.shape, order='F') - fImageD11.compute_gv( self.peaks_xyz, + gv = np.zeros(self.peaks_xyzT.shape, np.float ) + cImageD11.compute_gv( self.peaks_xyzT, self.cf.omega, self.transformpars.get('omegasign'), self.transformpars.get('wavelength'), @@ -232,7 +232,7 @@ def assign(self, ubi, translation, tol): self.transformpars.get('chi'), translation, gv) - hkl = np.dot( ubi, gv ) + hkl = np.dot( ubi, gv.T ) hkli = np.floor( hkl + 0.5 ) e = (hkl - hkli) e = (e*e).sum(axis=0) @@ -244,7 +244,7 @@ def assign(self, ubi, translation, tol): def gof( self, p, *args ): self.NC += 1 try: - hkls, inds, peaks_xyz, gobs, omega = args + hkls, inds, peaks_xyzT, gobs, omega = args except: print(args, len(args)) raise @@ -252,7 +252,7 @@ def gof( self, p, *args ): ub = p[:3] t = p[3] gcalc = np.dot( ub, hkls ) - fImageD11.compute_gv( peaks_xyz, + cImageD11.compute_gv( peaks_xyzT, omega, self.transformpars.get('omegasign'), self.transformpars.get('wavelength'), @@ -264,7 +264,7 @@ def gof( self, p, *args ): #print gcalc #print (gobs-gcalc).ravel() #1/0 - e = (gcalc - gobs).ravel() + e = (gcalc - gobs.T).ravel() p.shape = 12, # print p-0.1,(e*e).sum() return e#(e*e).sum() @@ -285,8 +285,8 @@ def refine(self, ubi, translation=(0,0,0) , ub = np.linalg.inv( ubi ) x0 = np.array( list( ub.ravel() ) + list(translation ) ) fun = self.gof - args = (hkls, inds, self.peaks_xyz[:,inds], - np.zeros( hkls.shape, order='F'), + args = (hkls, inds, self.peaks_xyzT[inds], + np.zeros(self.peaks_xyzT[inds].shape ), self.cf.omega[inds]) def Dfun( x0, *args ): epsilon = np.ones(12)*1e-6 @@ -319,7 +319,8 @@ def deriv( xk, f, epsilon, *args): c = columnfile( sys.argv[2] ) i = indexer( p, c ) if sys.argv[3][:3] == "fit": - # \test\simul_1000_grains>python ..\..\ImageD11\indexer.py Al1000\Al1000.par Al1000\Al1000.flt allgrid.map allgridfitscipy.map + # 0 1 2 3 4 5 + # \test\simul_1000_grains>python ..\..\ImageD11\indexer.py Al1000\Al1000.par Al1000\Al1000.flt fit allgrid.map allgridfitscipy.map gl = ImageD11.grain.read_grain_file( sys.argv[4] ) inds = np.arange( len(gl), dtype=np.int ) allhkls = np.array( (c.h, c.k, c.l) ) diff --git a/data/F21.spline 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0.4533741E+01 0.9318826E+01 + 0.2076617E+02 0.3722160E+02 0.5068682E+02 diff --git a/setup.py b/setup.py index 486dc3ae..35c87291 100644 --- a/setup.py +++ b/setup.py @@ -23,15 +23,11 @@ -# from distutils.core import setup, Extension -# from setuptools import setup, Extension import setuptools +import sys from numpy.distutils.core import setup, Extension - from numpy import get_include -nid = [get_include(),] -import sys if sys.platform == "win32" and "--compiler=mingw32" not in sys.argv: ecomparg = ["/openmp","-DF2PY_REPORT_ON_ARRAY_COPY"] @@ -43,8 +39,9 @@ elibs = ["gomp","pthread"] -# Compiled extensions: +nid = [get_include(),] +# Compiled extension: cImageD11extension = Extension( "cImageD11", sources = [ "src/cImageD11.pyf", "src/connectedpixels.c", @@ -58,30 +55,21 @@ ) - -import sys - -# New fortran code - you might regret this... -fi = Extension("fImageD11", - sources = ['fsrc/fImageD11.f90' ], - # This is always gcc/gfortran for now - extra_f90_compile_args=["-fopenmp -O2"], - libraries = elibs) - -# Remove list of dependencies from setup file +# Removed list of dependencies from setup file +# Do a miniconda (or something) instead... #if sys.platform == 'win32': # needed = [ # 'six', +# 'numpy>=1.0.0', +# 'scipy', # 'xfab>=0.0.2', +# 'pycifrw' # 'fabio>=0.0.5', -# 'numpy>=1.0.0', # 'matplotlib>=0.90.0', +# ... # ] -#else: # Take care of yourself if you are on linux needed = [] -# 'xfab>=0.0.1', -# 'fabio>=0.0.4'] # See the distutils docs... setup(name='ImageD11', @@ -91,13 +79,13 @@ description='ImageD11', license = "GPL", ext_package = "ImageD11", # Puts extensions in the ImageD11 directory - ext_modules = [cImageD11extension,fi], + ext_modules = [cImageD11extension,], install_requires = needed, packages = ["ImageD11"], package_dir = {"ImageD11":"ImageD11"}, url = "http://github.com/jonwright/ImageD11", # download_url = ["http://sourceforge.net/project/showfiles.php?group_id=82044&package_id=147869"], - package_data = {"ImageD11" : ["doc/*.html"]}, + package_data = {"ImageD11" : ["doc/*.html", "data/*" ]}, scripts = ["ImageD11/rsv_mapper.py", "scripts/peaksearch.py", "scripts/fitgrain.py", @@ -130,8 +118,4 @@ "scripts/avg_par.py", "scripts/powderimagetopeaks.py"]) -print("For windows you would need:") -print('set LDFLAGS="-static-libgfortran -static-libgcc -static -lgomp -shared"') -print('also gfortran/gcc installed (--compiler=mingw32)') -print('also to patch f2py to let it run') diff --git a/src/cdiffraction.c b/src/cdiffraction.c index 9fe236ee..609832a4 100644 --- a/src/cdiffraction.c +++ b/src/cdiffraction.c @@ -43,24 +43,28 @@ void compute_gv( double xlylzl[][3], double omega[], double omegasign, // ! Fill in rotation matrix of wedge, chi sw = sin(wedge*RAD); cw = cos(wedge*RAD); + wmat[0] = cw; wmat[1]=0.0; wmat[2]=-sw; + wmat[3] = 0.; wmat[4]=1.0; wmat[5]= 0.; + wmat[6] = sw; wmat[7]=0.0; wmat[8]= cw; sc = sin(chi*RAD); cc = cos(chi*RAD); - memcpy(wmat, (double[9]) {cw, 0., -sw, 0., 1., 0., sw, 0., cw}, - 9*sizeof(double)); - memcpy(cmat, (double[9]) {1., 0., 0., 0.,cc, -sc , 0.,sc, cc}, - 9*sizeof(double)); - // mat = matmul(cmat, wmat) + cmat[0] = 1.; cmat[1]=0.0; cmat[2]= 0.; + cmat[3] = 0.; cmat[4]= cc; cmat[5]=-sc; + cmat[6] = 0.; cmat[7]= sc; cmat[8]= cc; + // Combined mat = chi.wedge matmat(cmat, wmat, mat); #pragma omp parallel for private(so,co,u,o,d,modyz,ds,v,k) for(i=0;i