Changeset 952ea1f in sasview for src/sas/sascalc

Timestamp:

Oct 11, 2018 11:33:22 AM (6 years ago)

Author:

Paul Kienzle <pkienzle@…>

Branches:

master, magnetic_scatt, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249

Children:

7ba6470

Parents:

67ed543

git-author:

Paul Kienzle <pkienzle@…> (10/11/18 11:22:07)

git-committer:

Paul Kienzle <pkienzle@…> (10/11/18 11:33:22)

Message:

move c extensions from core/module.so to _module.so

Location:

src/sas/sascalc

Files:

• calculator/c_extensions/__init__.py (deleted)
• calculator/c_extensions/sld2i_module.c (modified) (2 diffs)
• calculator/sas_gen.py (modified) (5 diffs)
• file_converter/bsl_loader.py (modified) (2 diffs)
• file_converter/c_ext/__init__.py (deleted)
• file_converter/c_ext/bsl_loader.c (modified) (2 diffs)
• pr/c_extensions/Cinvertor.c (modified) (3 diffs)
• pr/c_extensions/__init__.py (deleted)
• pr/invertor.py (modified) (10 diffs)

src/sas/sascalc/calculator/c_extensions/sld2i_module.c

@@ -2 +2 @@
   SLD2I module to perform point and I calculations
  */
+#include <stdio.h>
+
+//#define Py_LIMITED_API 0x03020000
 #include <Python.h>
-#include <stdio.h>
+
 #include "sld2i.h"
 
@@ -160 +163 @@
 
 #define MODULE_DOC "Sld2i C Library"
-#define MODULE_NAME "sld2i"
-#define MODULE_INIT2 initsld2i
-#define MODULE_INIT3 PyInit_sld2i
+#define MODULE_NAME "_sld2i"
+#define MODULE_INIT2 init_sld2i
+#define MODULE_INIT3 PyInit__sld2i
 #define MODULE_METHODS module_methods
 

src/sas/sascalc/calculator/sas_gen.py

@@ -14 +14 @@
 import numpy as np
 
-from .core import sld2i as mod
+from . import _sld2i
 from .BaseComponent import BaseComponent
 
@@ -145 +145 @@
             self.params['Up_frac_out'],
             self.params['Up_theta'])
-        model = mod.new_GenI(*args)
+        model = _sld2i.new_GenI(*args)
         if len(qy):
             qx, qy = _vec(qx), _vec(qy)
             I_out = np.empty_like(qx)
             #print("npoints", qx.shape, "npixels", pos_x.shape)
-            mod.genicomXY(model, qx, qy, I_out)
+            _sld2i.genicomXY(model, qx, qy, I_out)
             #print("I_out after", I_out)
         else:
             qx = _vec(qx)
             I_out = np.empty_like(qx)
-            mod.genicom(model, qx, I_out)
+            _sld2i.genicom(model, qx, I_out)
         vol_correction = self.data_total_volume / self.params['total_volume']
         result = (self.params['scale'] * vol_correction * I_out
@@ -304 +304 @@
                 z_dir2 *= z_dir2
                 mask = (x_dir2 + y_dir2 + z_dir2) <= 1.0
-            except Exception:
-                logger.error(sys.exc_value)
+            except Exception as exc:
+                logger.error(exc)
         self.output = MagSLD(self.pos_x[mask], self.pos_y[mask],
                              self.pos_z[mask], self.sld_n[mask],
@@ -600 +600 @@
                         y_lines.append(y_line)
                         z_lines.append(z_line)
-                except Exception:
-                    logger.error(sys.exc_value)
+                except Exception as exc:
+                    logger.error(exc)
 
             output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
@@ -691 +691 @@
                             _vol_pix = float(toks[7])
                             vol_pix = np.append(vol_pix, _vol_pix)
-                        except Exception:
+                        except Exception as exc:
                             vol_pix = None
-                    except Exception:
+                    except Exception as exc:
                         # Skip non-data lines
-                        logger.error(sys.exc_value)
+                        logger.error(exc)
             output = MagSLD(pos_x, pos_y, pos_z, sld_n,
                             sld_mx, sld_my, sld_mz)

src/sas/sascalc/file_converter/bsl_loader.py

@@ -1 @@
-from sas.sascalc.file_converter.core.bsl_loader import CLoader
+from sas.sascalc.file_converter._bsl_loader import CLoader
 from sas.sascalc.dataloader.data_info import Data2D
 from copy import deepcopy
@@ -67 +67 @@
                     'swap_bytes': int(metadata[3])
                 }
-            except:
+            except Exception:
                 is_valid = False
                 err_msg = "Invalid metadata in header file for {}"

src/sas/sascalc/file_converter/c_ext/bsl_loader.c

@@ +1 @@
+#include <stdio.h>
+#include <stdlib.h>
+
+//#define Py_LIMITED_API 0x03020000
 #include <Python.h>
+#include <structmember.h>
 #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
 #include <numpy/arrayobject.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include "structmember.h"
+
 #include "bsl_loader.h"
 
@@ -292 +295 @@
 
 #define MODULE_DOC "C module for loading bsl."
-#define MODULE_NAME "bsl_loader"
-#define MODULE_INIT2 initbsl_loader
-#define MODULE_INIT3 PyInit_bsl_loader
+#define MODULE_NAME "_bsl_loader"
+#define MODULE_INIT2 init_bsl_loader
+#define MODULE_INIT3 PyInit__bsl_loader
 #define MODULE_METHODS module_methods
 

src/sas/sascalc/pr/c_extensions/Cinvertor.c

@@ -5 +5 @@
  *
  */
-#include <Python.h>
-#include "structmember.h"
 #include <stdio.h>
 #include <stdlib.h>
@@ -12 +10 @@
 #include <time.h>
 
+//#define Py_LIMITED_API 0x03050000
+#include <Python.h>
+#include <structmember.h>
+
 #include "invertor.h"
-
 
 /// Error object for raised exceptions
@@ -1121 +1122 @@
 
 #define MODULE_DOC "C extension module for inversion to P(r)."
-#define MODULE_NAME "pr_inversion"
-#define MODULE_INIT2 initpr_inversion
-#define MODULE_INIT3 PyInit_pr_inversion
+#define MODULE_NAME "_pr_inversion"
+#define MODULE_INIT2 init_pr_inversion
+#define MODULE_INIT3 PyInit__pr_inversion
 #define MODULE_METHODS module_methods
 

src/sas/sascalc/pr/invertor.py

@@ -17 +17 @@
 from numpy.linalg import lstsq
 from scipy import optimize
-from sas.sascalc.pr.core.pr_inversion import Cinvertor
+from sas.sascalc.pr._pr_inversion import Cinvertor
 
 logger = logging.getLogger(__name__)
@@ -71 +71 @@
         A[j][i] = (Fourier transformed base function for point j)
 
-    We them choose a number of r-points, n_r, to evaluate the second
+    We then choose a number of r-points, n_r, to evaluate the second
     derivative of P(r) at. This is used as our regularization term.
     For a vector r of length n_r, the following n_r rows are set to ::
@@ -144 +144 @@
         x, y, err, d_max, q_min, q_max and alpha
         """
-        if   name == 'x':
+        if name == 'x':
             if 0.0 in value:
                 msg = "Invertor: one of your q-values is zero. "
@@ -268 +268 @@
             A[i][j] = (Fourier transformed base function for point j)
 
-        We them choose a number of r-points, n_r, to evaluate the second
+        We then choose a number of r-points, n_r, to evaluate the second
         derivative of P(r) at. This is used as our regularization term.
         For a vector r of length n_r, the following n_r rows are set to ::
@@ -416 +416 @@
             A[i][j] = (Fourier transformed base function for point j)
 
-        We them choose a number of r-points, n_r, to evaluate the second
+        We then choose a number of r-points, n_r, to evaluate the second
         derivative of P(r) at. This is used as our regularization term.
         For a vector r of length n_r, the following n_r rows are set to ::
@@ -473 +473 @@
 
         # Perform the inversion (least square fit)
-        c, chi2, _, _ = lstsq(a, b)
+        c, chi2, _, _ = lstsq(a, b, rcond=None)
         # Sanity check
         try:
@@ -497 +497 @@
             cov = np.linalg.pinv(inv_cov)
             err = math.fabs(chi2 / float(npts - nfunc)) * cov
-        except:
+        except Exception as exc:
             # We were not able to estimate the errors
             # Return an empty error matrix
-            logger.error(sys.exc_value)
+            logger.error(exc)
 
         # Keep a copy of the last output
@@ -537 +537 @@
 
         """
-        from num_term import NTermEstimator
+        from .num_term import NTermEstimator
         estimator = NTermEstimator(self.clone())
         try:
             return estimator.num_terms(isquit_func)
-        except:
+        except Exception as exc:
             # If we fail, estimate alpha and return the default
             # number of terms
             best_alpha, _, _ = self.estimate_alpha(self.nfunc)
-            logger.warning("Invertor.estimate_numterms: %s" % sys.exc_value)
+            logger.warning("Invertor.estimate_numterms: %s" % exc)
             return self.nfunc, best_alpha, "Could not estimate number of terms"
 
@@ -631 +631 @@
                 return best_alpha, message, elapsed
 
-        except:
-            message = "Invertor.estimate_alpha: %s" % sys.exc_value
+        except Exception as exc:
+            message = "Invertor.estimate_alpha: %s" % exc
             return 0, message, elapsed
 
@@ -748 +748 @@
                         self.cov[i][i] = float(toks2[1])
 
-            except:
-                msg = "Invertor.from_file: corrupted file\n%s" % sys.exc_value
+            except Exception as exc:
+                msg = "Invertor.from_file: corrupted file\n%s" % exc
                 raise RuntimeError(msg)
         else: