- Timestamp:
- Oct 30, 2018 10:29:56 AM (6 years ago)
- Branches:
- master, magnetic_scatt, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249
- Children:
- 47be5a1, 895703d, f560e23, fee520ec
- Parents:
- 630aa5b (diff), 8e109f9 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent. - git-author:
- Paul Kienzle <pkienzle@…> (10/30/18 10:29:56)
- git-committer:
- GitHub <noreply@…> (10/30/18 10:29:56)
- Location:
- src/sas
- Files:
-
- 3 deleted
- 10 edited
-
sasgui/perspectives/fitting/gpu_options.py (modified) (6 diffs)
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sascalc/calculator/c_extensions/__init__.py (deleted)
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sascalc/calculator/c_extensions/sld2i_module.c (modified) (6 diffs)
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sascalc/calculator/sas_gen.py (modified) (5 diffs)
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sascalc/file_converter/bsl_loader.py (modified) (2 diffs)
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sascalc/file_converter/c_ext/__init__.py (deleted)
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sascalc/file_converter/c_ext/bsl_loader.c (modified) (2 diffs)
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sascalc/pr/c_extensions/Cinvertor.c (modified) (25 diffs)
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sascalc/pr/c_extensions/__init__.py (deleted)
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sascalc/pr/fit/BumpsFitting.py (modified) (2 diffs)
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sascalc/pr/fit/Loader.py (modified) (1 diff)
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sascalc/pr/invertor.py (modified) (11 diffs)
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sascalc/pr/num_term.py (modified) (3 diffs)
Legend:
- Unmodified
- Added
- Removed
-
src/sas/sasgui/perspectives/fitting/gpu_options.py
r388aefb r8e109f9 8 8 ''' 9 9 10 import json 11 import platform 10 12 import logging 11 13 import os 12 14 import sys 15 13 16 import wx 17 18 try: 19 import pyopencl as cl 20 except ImportError: 21 cl = None 22 14 23 import sasmodels 24 import sasmodels.model_test 25 import sasmodels.kernelcl 26 15 27 from sas.sasgui.guiframe.documentation_window import DocumentationWindow 16 28 … … 169 181 clinfo = [] 170 182 platforms = [] 171 try: 172 import pyopencl as cl 173 platforms = cl.get_platforms() 174 except ImportError: 183 184 if cl is None: 175 185 logger.warn("Unable to import the pyopencl package. It may not " 176 186 "have been installed. If you wish to use OpenCL, try " 177 187 "running pip install --user pyopencl") 178 except cl.LogicError as err: 179 logger.warn("Unable to fetch the OpenCL platforms. This likely " 180 "means that the opencl drivers for your system are " 181 "not installed.") 182 logger.warn(err) 188 else: 189 try: 190 platforms = cl.get_platforms() 191 except cl.LogicError as err: 192 logger.warn("Unable to fetch the OpenCL platforms. This likely " 193 "means that the opencl drivers for your system are " 194 "not installed.") 195 logger.warn(err) 183 196 184 197 p_index = 0 … … 226 239 if "SAS_OPENCL" in os.environ: 227 240 del os.environ["SAS_OPENCL"] 228 229 #Sasmodels kernelcl doesn't exist when initiated with None 230 if 'sasmodels.kernelcl' in sys.modules: 231 sasmodels.kernelcl.ENV = None 232 233 reload(sasmodels.core) 241 sasmodels.kernelcl.reset_environment() 234 242 event.Skip() 235 243 … … 247 255 Run sasmodels check from here and report results from 248 256 """ 249 import json250 import platform251 #import sasmodels252 253 257 #The same block of code as for OK but it is needed if we want to have 254 258 #active response to Test button … … 261 265 if "SAS_OPENCL" in os.environ: 262 266 del os.environ["SAS_OPENCL"] 263 264 #Sasmodels kernelcl doesn't exist when initiated with None 265 if 'sasmodels.kernelcl' in sys.modules: 266 sasmodels.kernelcl.ENV = None 267 268 269 #Need to reload sasmodels.core module to account SAS_OPENCL = "None" 270 reload(sasmodels.core) 271 272 273 from sasmodels.model_test import model_tests 267 sasmodels.kernelcl.reset_environment() 274 268 275 269 try: 276 from sasmodels.kernelcl import environment 277 env = environment() 270 env = sasmodels.kernelcl.environment() 278 271 clinfo = [(ctx.devices[0].platform.vendor, 279 272 ctx.devices[0].platform.version, … … 282 275 ctx.devices[0].version) 283 276 for ctx in env.context] 284 except ImportError:277 except Exception: 285 278 clinfo = None 286 279 287 280 failures = [] 288 281 tests_completed = 0 289 for test in model_tests():282 for test in sasmodels.model_test.model_tests(): 290 283 try: 291 284 test() -
src/sas/sascalc/calculator/c_extensions/sld2i_module.c
ra1daf86 r7ba6470 2 2 SLD2I module to perform point and I calculations 3 3 */ 4 #include <stdio.h> 5 6 //#define Py_LIMITED_API 0x03020000 4 7 #include <Python.h> 5 #include <stdio.h> 8 6 9 #include "sld2i.h" 7 10 … … 13 16 #endif 14 17 15 16 // Utilities 17 #define INVECTOR(obj,buf,len) \ 18 do { \ 19 int err = PyObject_AsReadBuffer(obj, (const void **)(&buf), &len); \ 20 if (err < 0) return NULL; \ 21 len /= sizeof(*buf); \ 22 } while (0) 23 24 #define OUTVECTOR(obj,buf,len) \ 25 do { \ 26 int err = PyObject_AsWriteBuffer(obj, (void **)(&buf), &len); \ 27 if (err < 0) return NULL; \ 28 len /= sizeof(*buf); \ 29 } while (0) 30 18 // Vector binding glue 19 #if (PY_VERSION_HEX > 0x03000000) && !defined(Py_LIMITED_API) 20 // Assuming that a view into a writable vector points to a 21 // non-changing pointer for the duration of the C call, capture 22 // the view pointer and immediately free the view. 23 #define VECTOR(VEC_obj, VEC_buf, VEC_len) do { \ 24 Py_buffer VEC_view; \ 25 int VEC_err = PyObject_GetBuffer(VEC_obj, &VEC_view, PyBUF_WRITABLE|PyBUF_FORMAT); \ 26 if (VEC_err < 0 || sizeof(*VEC_buf) != VEC_view.itemsize) return NULL; \ 27 VEC_buf = (typeof(VEC_buf))VEC_view.buf; \ 28 VEC_len = VEC_view.len/sizeof(*VEC_buf); \ 29 PyBuffer_Release(&VEC_view); \ 30 } while (0) 31 #else 32 #define VECTOR(VEC_obj, VEC_buf, VEC_len) do { \ 33 int VEC_err = PyObject_AsWriteBuffer(VEC_obj, (void **)(&VEC_buf), &VEC_len); \ 34 if (VEC_err < 0) return NULL; \ 35 VEC_len /= sizeof(*VEC_buf); \ 36 } while (0) 37 #endif 31 38 32 39 /** … … 73 80 //printf("new GenI\n"); 74 81 if (!PyArg_ParseTuple(args, "iOOOOOOOOddd", &is_avg, &x_val_obj, &y_val_obj, &z_val_obj, &sldn_val_obj, &mx_val_obj, &my_val_obj, &mz_val_obj, &vol_pix_obj, &inspin, &outspin, &stheta)) return NULL; 75 INVECTOR(x_val_obj, x_val, n_x);76 INVECTOR(y_val_obj, y_val, n_y);77 INVECTOR(z_val_obj, z_val, n_z);78 INVECTOR(sldn_val_obj, sldn_val, n_sld);79 INVECTOR(mx_val_obj, mx_val, n_mx);80 INVECTOR(my_val_obj, my_val, n_my);81 INVECTOR(mz_val_obj, mz_val, n_mz);82 INVECTOR(vol_pix_obj, vol_pix, n_vol_pix);82 VECTOR(x_val_obj, x_val, n_x); 83 VECTOR(y_val_obj, y_val, n_y); 84 VECTOR(z_val_obj, z_val, n_z); 85 VECTOR(sldn_val_obj, sldn_val, n_sld); 86 VECTOR(mx_val_obj, mx_val, n_mx); 87 VECTOR(my_val_obj, my_val, n_my); 88 VECTOR(mz_val_obj, mz_val, n_mz); 89 VECTOR(vol_pix_obj, vol_pix, n_vol_pix); 83 90 sld2i = PyMem_Malloc(sizeof(GenI)); 84 91 //printf("sldi:%p\n", sld2i); … … 108 115 if (!PyArg_ParseTuple(args, "OOOO", &gen_obj, &qx_obj, &qy_obj, &I_out_obj)) return NULL; 109 116 sld2i = (GenI *)PyCapsule_GetPointer(gen_obj, "GenI"); 110 INVECTOR(qx_obj, qx, n_qx);111 INVECTOR(qy_obj, qy, n_qy);112 OUTVECTOR(I_out_obj, I_out, n_out);117 VECTOR(qx_obj, qx, n_qx); 118 VECTOR(qy_obj, qy, n_qy); 119 VECTOR(I_out_obj, I_out, n_out); 113 120 //printf("qx, qy, I_out: %d %d %d, %d %d %d\n", qx, qy, I_out, n_qx, n_qy, n_out); 114 121 … … 136 143 if (!PyArg_ParseTuple(args, "OOO", &gen_obj, &q_obj, &I_out_obj)) return NULL; 137 144 sld2i = (GenI *)PyCapsule_GetPointer(gen_obj, "GenI"); 138 INVECTOR(q_obj, q, n_q);139 OUTVECTOR(I_out_obj, I_out, n_out);145 VECTOR(q_obj, q, n_q); 146 VECTOR(I_out_obj, I_out, n_out); 140 147 141 148 // Sanity check … … 160 167 161 168 #define MODULE_DOC "Sld2i C Library" 162 #define MODULE_NAME " sld2i"163 #define MODULE_INIT2 init sld2i164 #define MODULE_INIT3 PyInit_ sld2i169 #define MODULE_NAME "_sld2i" 170 #define MODULE_INIT2 init_sld2i 171 #define MODULE_INIT3 PyInit__sld2i 165 172 #define MODULE_METHODS module_methods 166 173 -
src/sas/sascalc/calculator/sas_gen.py
r144e032a r952ea1f 14 14 import numpy as np 15 15 16 from . core import sld2i as mod16 from . import _sld2i 17 17 from .BaseComponent import BaseComponent 18 18 … … 145 145 self.params['Up_frac_out'], 146 146 self.params['Up_theta']) 147 model = mod.new_GenI(*args)147 model = _sld2i.new_GenI(*args) 148 148 if len(qy): 149 149 qx, qy = _vec(qx), _vec(qy) 150 150 I_out = np.empty_like(qx) 151 151 #print("npoints", qx.shape, "npixels", pos_x.shape) 152 mod.genicomXY(model, qx, qy, I_out)152 _sld2i.genicomXY(model, qx, qy, I_out) 153 153 #print("I_out after", I_out) 154 154 else: 155 155 qx = _vec(qx) 156 156 I_out = np.empty_like(qx) 157 mod.genicom(model, qx, I_out)157 _sld2i.genicom(model, qx, I_out) 158 158 vol_correction = self.data_total_volume / self.params['total_volume'] 159 159 result = (self.params['scale'] * vol_correction * I_out … … 304 304 z_dir2 *= z_dir2 305 305 mask = (x_dir2 + y_dir2 + z_dir2) <= 1.0 306 except Exception :307 logger.error( sys.exc_value)306 except Exception as exc: 307 logger.error(exc) 308 308 self.output = MagSLD(self.pos_x[mask], self.pos_y[mask], 309 309 self.pos_z[mask], self.sld_n[mask], … … 600 600 y_lines.append(y_line) 601 601 z_lines.append(z_line) 602 except Exception :603 logger.error( sys.exc_value)602 except Exception as exc: 603 logger.error(exc) 604 604 605 605 output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz) … … 691 691 _vol_pix = float(toks[7]) 692 692 vol_pix = np.append(vol_pix, _vol_pix) 693 except Exception :693 except Exception as exc: 694 694 vol_pix = None 695 except Exception :695 except Exception as exc: 696 696 # Skip non-data lines 697 logger.error( sys.exc_value)697 logger.error(exc) 698 698 output = MagSLD(pos_x, pos_y, pos_z, sld_n, 699 699 sld_mx, sld_my, sld_mz) -
src/sas/sascalc/file_converter/bsl_loader.py
rf00691d4 r952ea1f 1 from sas.sascalc.file_converter. core.bsl_loader import CLoader1 from sas.sascalc.file_converter._bsl_loader import CLoader 2 2 from sas.sascalc.dataloader.data_info import Data2D 3 3 from copy import deepcopy … … 67 67 'swap_bytes': int(metadata[3]) 68 68 } 69 except :69 except Exception: 70 70 is_valid = False 71 71 err_msg = "Invalid metadata in header file for {}" -
src/sas/sascalc/file_converter/c_ext/bsl_loader.c
rd5aeaa3 r952ea1f 1 #include <stdio.h> 2 #include <stdlib.h> 3 4 //#define Py_LIMITED_API 0x03020000 1 5 #include <Python.h> 6 #include <structmember.h> 2 7 #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION 3 8 #include <numpy/arrayobject.h> 4 #include <stdio.h> 5 #include <stdlib.h> 6 #include "structmember.h" 9 7 10 #include "bsl_loader.h" 8 11 … … 292 295 293 296 #define MODULE_DOC "C module for loading bsl." 294 #define MODULE_NAME " bsl_loader"295 #define MODULE_INIT2 init bsl_loader296 #define MODULE_INIT3 PyInit_ bsl_loader297 #define MODULE_NAME "_bsl_loader" 298 #define MODULE_INIT2 init_bsl_loader 299 #define MODULE_INIT3 PyInit__bsl_loader 297 300 #define MODULE_METHODS module_methods 298 301 -
src/sas/sascalc/pr/c_extensions/Cinvertor.c
ra52f32f r7ba6470 5 5 * 6 6 */ 7 #include <Python.h>8 #include "structmember.h"9 7 #include <stdio.h> 10 8 #include <stdlib.h> … … 12 10 #include <time.h> 13 11 12 //#define Py_LIMITED_API 0x03050000 13 #include <Python.h> 14 #include <structmember.h> 15 16 // Vector binding glue 17 #if (PY_VERSION_HEX > 0x03000000) && !defined(Py_LIMITED_API) 18 // Assuming that a view into a writable vector points to a 19 // non-changing pointer for the duration of the C call, capture 20 // the view pointer and immediately free the view. 21 #define VECTOR(VEC_obj, VEC_buf, VEC_len) do { \ 22 Py_buffer VEC_view; \ 23 int VEC_err = PyObject_GetBuffer(VEC_obj, &VEC_view, PyBUF_WRITABLE|PyBUF_FORMAT); \ 24 if (VEC_err < 0 || sizeof(*VEC_buf) != VEC_view.itemsize) return NULL; \ 25 VEC_buf = (typeof(VEC_buf))VEC_view.buf; \ 26 VEC_len = VEC_view.len/sizeof(*VEC_buf); \ 27 PyBuffer_Release(&VEC_view); \ 28 } while (0) 29 #else 30 #define VECTOR(VEC_obj, VEC_buf, VEC_len) do { \ 31 int VEC_err = PyObject_AsWriteBuffer(VEC_obj, (void **)(&VEC_buf), &VEC_len); \ 32 if (VEC_err < 0) return NULL; \ 33 VEC_len /= sizeof(*VEC_buf); \ 34 } while (0) 35 #endif 36 14 37 #include "invertor.h" 15 16 38 17 39 /// Error object for raised exceptions 18 40 PyObject * CinvertorError; 19 20 #define INVECTOR(obj,buf,len) \21 do { \22 int err = PyObject_AsReadBuffer(obj, (const void **)(&buf), &len); \23 if (err < 0) return NULL; \24 len /= sizeof(*buf); \25 } while (0)26 27 #define OUTVECTOR(obj,buf,len) \28 do { \29 int err = PyObject_AsWriteBuffer(obj, (void **)(&buf), &len); \30 if (err < 0) return NULL; \31 len /= sizeof(*buf); \32 } while (0)33 34 41 35 42 // Class definition … … 99 106 100 107 if (!PyArg_ParseTuple(args, "O", &data_obj)) return NULL; 101 OUTVECTOR(data_obj,data,ndata);108 VECTOR(data_obj,data,ndata); 102 109 103 110 free(self->params.x); … … 131 138 132 139 if (!PyArg_ParseTuple(args, "O", &data_obj)) return NULL; 133 OUTVECTOR(data_obj, data, ndata);140 VECTOR(data_obj, data, ndata); 134 141 135 142 // Check that the input array is large enough … … 164 171 165 172 if (!PyArg_ParseTuple(args, "O", &data_obj)) return NULL; 166 OUTVECTOR(data_obj,data,ndata);173 VECTOR(data_obj,data,ndata); 167 174 168 175 free(self->params.y); … … 196 203 197 204 if (!PyArg_ParseTuple(args, "O", &data_obj)) return NULL; 198 OUTVECTOR(data_obj, data, ndata);205 VECTOR(data_obj, data, ndata); 199 206 200 207 // Check that the input array is large enough … … 229 236 230 237 if (!PyArg_ParseTuple(args, "O", &data_obj)) return NULL; 231 OUTVECTOR(data_obj,data,ndata);238 VECTOR(data_obj,data,ndata); 232 239 233 240 free(self->params.err); … … 261 268 262 269 if (!PyArg_ParseTuple(args, "O", &data_obj)) return NULL; 263 OUTVECTOR(data_obj, data, ndata);270 VECTOR(data_obj, data, ndata); 264 271 265 272 // Check that the input array is large enough … … 517 524 if (!PyArg_ParseTuple(args, "O", &data_obj)) return NULL; 518 525 519 OUTVECTOR(data_obj,pars,npars);526 VECTOR(data_obj,pars,npars); 520 527 521 528 // PyList of residuals … … 568 575 if (!PyArg_ParseTuple(args, "O", &data_obj)) return NULL; 569 576 570 OUTVECTOR(data_obj,pars,npars);577 VECTOR(data_obj,pars,npars); 571 578 572 579 // Should create this list only once and refill it … … 609 616 610 617 if (!PyArg_ParseTuple(args, "Od", &data_obj, &q)) return NULL; 611 OUTVECTOR(data_obj,pars,npars);618 VECTOR(data_obj,pars,npars); 612 619 613 620 iq_value = iq(pars, self->params.d_max, (int)npars, q); … … 634 641 635 642 if (!PyArg_ParseTuple(args, "Od", &data_obj, &q)) return NULL; 636 OUTVECTOR(data_obj,pars,npars);643 VECTOR(data_obj,pars,npars); 637 644 638 645 iq_value = iq_smeared(pars, self->params.d_max, (int)npars, … … 659 666 660 667 if (!PyArg_ParseTuple(args, "Od", &data_obj, &r)) return NULL; 661 OUTVECTOR(data_obj,pars,npars);668 VECTOR(data_obj,pars,npars); 662 669 663 670 pr_value = pr(pars, self->params.d_max, (int)npars, r); … … 686 693 687 694 if (!PyArg_ParseTuple(args, "OOd", &data_obj, &err_obj, &r)) return NULL; 688 OUTVECTOR(data_obj,pars,npars);695 VECTOR(data_obj,pars,npars); 689 696 690 697 if (err_obj == Py_None) { … … 692 699 pr_err_value = 0.0; 693 700 } else { 694 OUTVECTOR(err_obj,pars_err,npars2);701 VECTOR(err_obj,pars_err,npars2); 695 702 pr_err(pars, pars_err, self->params.d_max, (int)npars, r, &pr_value, &pr_err_value); 696 703 } … … 726 733 727 734 if (!PyArg_ParseTuple(args, "O", &data_obj)) return NULL; 728 OUTVECTOR(data_obj,pars,npars);735 VECTOR(data_obj,pars,npars); 729 736 730 737 oscill = reg_term(pars, self->params.d_max, (int)npars, 100); … … 747 754 748 755 if (!PyArg_ParseTuple(args, "O", &data_obj)) return NULL; 749 OUTVECTOR(data_obj,pars,npars);756 VECTOR(data_obj,pars,npars); 750 757 751 758 count = npeaks(pars, self->params.d_max, (int)npars, 100); … … 768 775 769 776 if (!PyArg_ParseTuple(args, "O", &data_obj)) return NULL; 770 OUTVECTOR(data_obj,pars,npars);777 VECTOR(data_obj,pars,npars); 771 778 772 779 fraction = positive_integral(pars, self->params.d_max, (int)npars, 100); … … 792 799 793 800 if (!PyArg_ParseTuple(args, "OO", &data_obj, &err_obj)) return NULL; 794 OUTVECTOR(data_obj,pars,npars);795 OUTVECTOR(err_obj,pars_err,npars2);801 VECTOR(data_obj,pars,npars); 802 VECTOR(err_obj,pars_err,npars2); 796 803 797 804 fraction = positive_errors(pars, pars_err, self->params.d_max, (int)npars, 51); … … 813 820 814 821 if (!PyArg_ParseTuple(args, "O", &data_obj)) return NULL; 815 OUTVECTOR(data_obj,pars,npars);822 VECTOR(data_obj,pars,npars); 816 823 817 824 value = rg(pars, self->params.d_max, (int)npars, 101); … … 833 840 834 841 if (!PyArg_ParseTuple(args, "O", &data_obj)) return NULL; 835 OUTVECTOR(data_obj,pars,npars);842 VECTOR(data_obj,pars,npars); 836 843 837 844 value = 4.0*acos(-1.0)*int_pr(pars, self->params.d_max, (int)npars, 101); … … 874 881 875 882 if (!PyArg_ParseTuple(args, "iiOO", &nfunc, &nr, &a_obj, &b_obj)) return NULL; 876 OUTVECTOR(a_obj,a,n_a);877 OUTVECTOR(b_obj,b,n_b);883 VECTOR(a_obj,a,n_a); 884 VECTOR(b_obj,b,n_b); 878 885 879 886 assert(n_b>=nfunc); … … 947 954 948 955 if (!PyArg_ParseTuple(args, "iiOO", &nfunc, &nr, &a_obj, &cov_obj)) return NULL; 949 OUTVECTOR(a_obj,a,n_a);950 OUTVECTOR(cov_obj,inv_cov,n_cov);956 VECTOR(a_obj,a,n_a); 957 VECTOR(cov_obj,inv_cov,n_cov); 951 958 952 959 assert(n_cov>=nfunc*nfunc); … … 981 988 982 989 if (!PyArg_ParseTuple(args, "iiO", &nfunc, &nr, &a_obj)) return NULL; 983 OUTVECTOR(a_obj,a,n_a);990 VECTOR(a_obj,a,n_a); 984 991 985 992 assert(n_a>=nfunc*(nr+self->params.npoints)); … … 1121 1128 1122 1129 #define MODULE_DOC "C extension module for inversion to P(r)." 1123 #define MODULE_NAME " pr_inversion"1124 #define MODULE_INIT2 init pr_inversion1125 #define MODULE_INIT3 PyInit_ pr_inversion1130 #define MODULE_NAME "_pr_inversion" 1131 #define MODULE_INIT2 init_pr_inversion 1132 #define MODULE_INIT3 PyInit__pr_inversion 1126 1133 #define MODULE_METHODS module_methods 1127 1134 -
src/sas/sascalc/pr/fit/BumpsFitting.py
r9a5097c r3e6829d 2 2 BumpsFitting module runs the bumps optimizer. 3 3 """ 4 from __future__ import division 5 4 6 import os 5 7 from datetime import timedelta, datetime … … 34 36 class Progress(object): 35 37 def __init__(self, history, max_step, pars, dof): 36 remaining_time = int(history.time[0]*( float(max_step)/history.step[0]-1))38 remaining_time = int(history.time[0]*(max_step/history.step[0]-1)) 37 39 # Depending on the time remaining, either display the expected 38 40 # time of completion, or the amount of time remaining. Use precision -
src/sas/sascalc/pr/fit/Loader.py
r574adc7 r57e48ca 1 """ 2 class Loader to load any kind of file 3 """ 4 1 5 from __future__ import print_function 2 6 3 # class Loader to load any king of file4 #import wx5 #import string6 7 import numpy as np 7 8 -
src/sas/sascalc/pr/invertor.py
r2469df7 r57e48ca 6 6 FIXME: The way the Invertor interacts with its C component should be cleaned up 7 7 """ 8 from __future__ import division 8 9 9 10 import numpy as np … … 17 18 from numpy.linalg import lstsq 18 19 from scipy import optimize 19 from sas.sascalc.pr. core.pr_inversion import Cinvertor20 from sas.sascalc.pr._pr_inversion import Cinvertor 20 21 21 22 logger = logging.getLogger(__name__) … … 71 72 A[j][i] = (Fourier transformed base function for point j) 72 73 73 We the mchoose a number of r-points, n_r, to evaluate the second74 We then choose a number of r-points, n_r, to evaluate the second 74 75 derivative of P(r) at. This is used as our regularization term. 75 76 For a vector r of length n_r, the following n_r rows are set to :: … … 144 145 x, y, err, d_max, q_min, q_max and alpha 145 146 """ 146 if 147 if name == 'x': 147 148 if 0.0 in value: 148 149 msg = "Invertor: one of your q-values is zero. " … … 268 269 A[i][j] = (Fourier transformed base function for point j) 269 270 270 We the mchoose a number of r-points, n_r, to evaluate the second271 We then choose a number of r-points, n_r, to evaluate the second 271 272 derivative of P(r) at. This is used as our regularization term. 272 273 For a vector r of length n_r, the following n_r rows are set to :: … … 416 417 A[i][j] = (Fourier transformed base function for point j) 417 418 418 We the mchoose a number of r-points, n_r, to evaluate the second419 We then choose a number of r-points, n_r, to evaluate the second 419 420 derivative of P(r) at. This is used as our regularization term. 420 421 For a vector r of length n_r, the following n_r rows are set to :: … … 473 474 474 475 # Perform the inversion (least square fit) 475 c, chi2, _, _ = lstsq(a, b )476 c, chi2, _, _ = lstsq(a, b, rcond=-1) 476 477 # Sanity check 477 478 try: … … 496 497 try: 497 498 cov = np.linalg.pinv(inv_cov) 498 err = math.fabs(chi2 / float(npts - nfunc)) * cov499 except :499 err = math.fabs(chi2 / (npts - nfunc)) * cov 500 except Exception as exc: 500 501 # We were not able to estimate the errors 501 502 # Return an empty error matrix 502 logger.error( sys.exc_value)503 logger.error(exc) 503 504 504 505 # Keep a copy of the last output … … 537 538 538 539 """ 539 from num_term import NTermEstimator540 from .num_term import NTermEstimator 540 541 estimator = NTermEstimator(self.clone()) 541 542 try: 542 543 return estimator.num_terms(isquit_func) 543 except :544 except Exception as exc: 544 545 # If we fail, estimate alpha and return the default 545 546 # number of terms 546 547 best_alpha, _, _ = self.estimate_alpha(self.nfunc) 547 logger.warning("Invertor.estimate_numterms: %s" % sys.exc_value)548 logger.warning("Invertor.estimate_numterms: %s" % exc) 548 549 return self.nfunc, best_alpha, "Could not estimate number of terms" 549 550 … … 631 632 return best_alpha, message, elapsed 632 633 633 except :634 message = "Invertor.estimate_alpha: %s" % sys.exc_value634 except Exception as exc: 635 message = "Invertor.estimate_alpha: %s" % exc 635 636 return 0, message, elapsed 636 637 … … 748 749 self.cov[i][i] = float(toks2[1]) 749 750 750 except :751 msg = "Invertor.from_file: corrupted file\n%s" % sys.exc_value751 except Exception as exc: 752 msg = "Invertor.from_file: corrupted file\n%s" % exc 752 753 raise RuntimeError(msg) 753 754 else: -
src/sas/sascalc/pr/num_term.py
r2469df7 r3e6829d 1 from __future__ import print_function 1 from __future__ import print_function, division 2 2 3 3 import math … … 51 51 osc = self.sort_osc() 52 52 dv = len(osc) 53 med = float(dv) / 2.053 med = 0.5*dv 54 54 odd = self.is_odd(dv) 55 55 medi = 0 … … 140 140 nts = self.compare_err() 141 141 div = len(nts) 142 tem = float(div) / 2.0142 tem = 0.5*div 143 143 if self.is_odd(div): 144 144 nt = nts[int(tem)]
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