Merge branch 'do_not_shadow_dir' into 'NIFTy_7'

Do not shadow native `dir`; rename to `direction`

See merge request !596

src/extra.py

@@ -291,22 +291,22 @@ def _performance_check(op, pos, raise_on_fail):
 def _get_acceptable_location(op, loc, lin):
     if not np.isfinite(lin.val.s_sum()):
         raise ValueError('Initial value must be finite')
-    dir = from_random(loc.domain, dtype=loc.dtype)
-    dirder = lin.jac(dir)
+    direction = from_random(loc.domain, dtype=loc.dtype)
+    dirder = lin.jac(direction)
     if dirder.norm() == 0:
-        dir = dir * (lin.val.norm()*1e-5)
+        direction = direction * (lin.val.norm() * 1e-5)
     else:
-        dir = dir * (lin.val.norm()*1e-5/dirder.norm())
+        direction = direction * (lin.val.norm() * 1e-5 / dirder.norm())
     # Find a step length that leads to a "reasonable" location
     for i in range(50):
         try:
-            loc2 = loc+dir
+            loc2 = loc + direction
             lin2 = op(Linearization.make_var(loc2, lin.want_metric))
             if np.isfinite(lin2.val.s_sum()) and abs(lin2.val.s_sum()) < 1e20:
                 break
         except FloatingPointError:
             pass
-        dir = dir*0.5
+        direction = direction * 0.5
     else:
         raise ValueError("could not find a reasonable initial step")
     return loc2, lin2
@@ -368,21 +368,21 @@ def _jac_vs_finite_differences(op, loc, tol, ntries, only_r_differentiable):
     for _ in range(ntries):
         lin = op(Linearization.make_var(loc))
         loc2, lin2 = _get_acceptable_location(op, loc, lin)
-        dir = loc2-loc
+        direction = loc2 - loc
         locnext = loc2
-        dirnorm = dir.norm()
+        dirnorm = direction.norm()
         hist = []
         for i in range(50):
-            locmid = loc + 0.5*dir
+            locmid = loc + 0.5 * direction
             linmid = op(Linearization.make_var(locmid))
-            dirder = linmid.jac(dir)
-            numgrad = (lin2.val-lin.val)
+            dirder = linmid.jac(direction)
+            numgrad = (lin2.val - lin.val)
             xtol = tol * dirder.norm() / np.sqrt(dirder.size)
-            hist.append((numgrad-dirder).norm())
-#            print(len(hist),hist[-1])
-            if (abs(numgrad-dirder) <= xtol).s_all():
+            hist.append((numgrad - dirder).norm())
+            # print(len(hist),hist[-1])
+            if (abs(numgrad - dirder) <= xtol).s_all():
                 break
-            dir = dir*0.5
+            direction = direction * 0.5
             dirnorm *= 0.5
             loc2, lin2 = locmid, linmid
         else:

src/library/los_response.py

@@ -42,11 +42,11 @@ def _comp_traverse(start, end, shp, dist, lo, mid, hi, sig, erf):
 
     out = [None]*nlos
     for i in range(nlos):
-        dir = end[:, i]-start[:, i]
-        dirx = np.where(dir == 0., 1e-12, dir)
-        d0 = np.where(dir == 0., ((start[:, i] > 0)-0.5)*1e12,
+        direction = end[:, i]-start[:, i]
+        dirx = np.where(direction == 0., 1e-12, direction)
+        d0 = np.where(direction == 0., ((start[:, i] > 0)-0.5)*1e12,
                       -start[:, i]/dirx)
-        d1 = np.where(dir == 0., ((start[:, i] < pmax)-0.5)*-1e12,
+        d1 = np.where(direction == 0., ((start[:, i] < pmax)-0.5)*-1e12,
                       (pmax-start[:, i])/dirx)
         (dmin, dmax) = (np.minimum(d0, d1), np.maximum(d0, d1))
         dmin = dmin.max()
@@ -61,18 +61,18 @@ def _comp_traverse(start, end, shp, dist, lo, mid, hi, sig, erf):
             out[i] = (np.full(0, 0, dtype=np.int64), np.full(0, 0.))
             continue
         # determine coordinates of first cell crossing
-        c_first = np.ceil(start[:, i]+dir*dmin)
-        c_first = np.where(dir > 0., c_first, c_first-1.)
+        c_first = np.ceil(start[:, i]+direction*dmin)
+        c_first = np.where(direction > 0., c_first, c_first-1.)
         c_first = (c_first-start[:, i])/dirx
-        pos1 = np.asarray((start[:, i]+dmin*dir), dtype=np.int)
+        pos1 = np.asarray((start[:, i]+dmin*direction), dtype=np.int)
         pos1 = np.sum(pos1*inc)
         cdist = np.empty(0, dtype=np.float64)
         add = np.empty(0, dtype=np.int)
         for j in range(ndim):
-            if dir[j] != 0:
-                step = inc[j] if dir[j] > 0 else -inc[j]
+            if direction[j] != 0:
+                step = inc[j] if direction[j] > 0 else -inc[j]
                 tmp = np.arange(start=c_first[j], stop=dmax,
-                                step=abs(1./dir[j]))
+                                step=abs(1./direction[j]))
                 cdist = np.append(cdist, tmp)
                 add = np.append(add, np.full(len(tmp), step, dtype=np.int64))
         idx = np.argsort(cdist)
@@ -80,7 +80,7 @@ def _comp_traverse(start, end, shp, dist, lo, mid, hi, sig, erf):
         add = add[idx]
         cdist = np.append(np.full(1, dmin), cdist)
         cdist = np.append(cdist, np.full(1, dmax))
-        corfac = np.linalg.norm(dir*dist)
+        corfac = np.linalg.norm(direction*dist)
         cdist *= corfac
         wgt = np.diff(cdist)
         mdist = 0.5*(cdist[:-1]+cdist[1:])

src/minimization/energy.py

@@ -119,18 +119,18 @@ class Energy(metaclass=NiftyMeta):
         """
         raise NotImplementedError
 
-    def longest_step(self, dir):
-        """Returns the longest allowed step size along `dir`
+    def longest_step(self, direction):
+        """Returns the longest allowed step size along `direction`
 
         Parameters
         ----------
-        dir : Field
+        direction : Field
             the search direction
 
         Returns
         -------
         float or None
             the longest allowed step when starting from `self.position` along
-            `dir`. If None, the step size is not limited.
+            `direction`. If None, the step size is not limited.
         """
         return None

src/operators/energy_operators.py

@@ -242,7 +242,7 @@ class GaussianEnergy(EnergyOperator):
         not. Note that for a complex Gaussian the inverse_covariance is
         .. math ::
         (<ff^dagger>)^{-1}_P(f)/2,
-        where the additional factor of 2 is necessary because the 
+        where the additional factor of 2 is necessary because the
         domain of s has double as many dimensions as in the real case.
 
     Note