Changeset 952ea1f in sasview for src/sas/sascalc/pr

Timestamp:

Oct 11, 2018 1:33:22 PM (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 13:22:07)

git-committer:

Paul Kienzle <pkienzle@…> (10/11/18 13:33:22)

Message:

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

Location:

src/sas/sascalc/pr

Files:

• c_extensions/Cinvertor.c (modified) (3 diffs)
• c_extensions/__init__.py (deleted)
• invertor.py (modified) (10 diffs)

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: