Replacing print statements with logging statements

pyknotid/representations/gausscode.py

@@ -15,6 +15,7 @@
 import numpy as n
 import re
 import sys
+import logging
 
 
 class GaussCode(object):
@@ -101,7 +102,7 @@ def calculating_orientations(cls, code):
         from pyknotid.representations import representation
         rep = representation.Representation(gc)
         # rep.draw_planar_graph()
-        # print('ready to do space curve')
+        # logging.info('ready to do space curve')
         sp = rep.space_curve()
         # sp.rotate()
         return sp.gauss_code()
@@ -271,7 +272,6 @@ def _do_reidemeister_moves(self, one=True, two=True, one_extended=True):
         # Next do RM1_extended separately (could be more efficient?)
         if one_extended:
             # Do extended RM1 as a separate step
-            print
             code = [(line[keep] if len(line) > 0 else line) for (line, keep) in zip(code, keeps)]
             keeps = [n.ones(l.shape[0], dtype=bool) for l in code]
 
@@ -365,7 +365,7 @@ def simplify(self, one=True, two=True, one_extended=True):
         '''
 
         if self.verbose:
-            print('Simplifying: initially {} crossings'.format(
+            logging.info('Simplifying: initially {} crossings'.format(
                 n.sum([len(line) for line in self._gauss_code])))
 
         number_of_runs = 0
@@ -377,15 +377,11 @@ def simplify(self, one=True, two=True, one_extended=True):
             new_len = n.sum([len(line) for line in new_gc])
             number_of_runs += 1
             if self.verbose:
-                sys.stdout.write('\r-> {} crossings after {} runs'.format(
+                logging.info('\r-> {} crossings after {} runs'.format(
                     n.sum([len(line) for line in new_gc]), number_of_runs))
-                sys.stdout.flush()
             if new_len == original_len:
                 break
 
-        if self.verbose:
-            print()
-
     def reindex_crossings(self):
         '''Replaces the indices of the crossings in the Gauss code with the
         integers from 1 to its length.
@@ -429,4 +425,3 @@ def _get_crossing_numbers(gc):
         for entry in line:
             crossing_vals.add(entry[0])
     return crossing_vals
-

pyknotid/spacecurves/link.py

@@ -25,9 +25,10 @@
 from pyknotid.spacecurves import helpers
 from pyknotid.spacecurves.knot import Knot
 from pyknotid.visualise import plot_projection
-from pyknotid.utils import (vprint, get_rotation_matrix,
+from pyknotid.utils import (get_rotation_matrix,
                            ensure_shape_tuple)
 
+import logging
 
 class Link(object):
     '''
@@ -169,7 +170,7 @@ def raw_crossings(self, mode='use_max_jump', only_with_other_lines=True,
         if only_with_other_lines:
             crossings = [[] for _ in lines]
         else:
-            self._vprint('Calculating self-crossings for all {} '
+            logging.info('Calculating self-crossings for all {} '
                          'component lines'.format(len(lines)))
             crossings = [k.raw_crossings(
                 mode=mode, include_closure=include_closures,
@@ -197,7 +198,7 @@ def raw_crossings(self, mode='use_max_jump', only_with_other_lines=True,
 
         for line_index, line in enumerate(lines):
             for other_index, other_line in enumerate(lines[line_index+1:]):
-                self._vprint(
+                logging.info(
                     '\rComparing line {} with {}'.format(line_index,
                                                          other_index))
 
@@ -219,7 +220,7 @@ def raw_crossings(self, mode='use_max_jump', only_with_other_lines=True,
 
                 for i in first_line_range:
                     if i % 1000 == 0:
-                        self._vprint(
+                        logging.info(
                             '\ri = {} / {}'.format(
                                 i, len(first_line_range)), False)
                     v0 = points[i]
@@ -246,7 +247,7 @@ def raw_crossings(self, mode='use_max_jump', only_with_other_lines=True,
                     crossings[line_index].extend(first_crossings.tolist())
                     crossings[other_index].extend(sec_crossings.tolist())
 
-        self._vprint('\n{} crossings found\n'.format(
+        logging.info('\n{} crossings found\n'.format(
             [len(cs) / 2 for cs in crossings]))
         [cs.sort(key=lambda s: s[0]) for cs in crossings]
         crossings = [n.array(cs) for cs in crossings]
@@ -386,7 +387,7 @@ def octree_simplify(self, runs=1, plot=False, rotate=True,
             line.points = remove_nearby_points(line.points)
         for i in range(runs):
             if n.sum([len(knot.points) for knot in self.lines]) > 30:
-                vprint('\rRun {} of {}, {} points remain'.format(
+                logging.info('\rRun {} of {}, {} points remain'.format(
                     i, runs, len(self)), False, self.verbose)
 
             if rotate:
@@ -409,7 +410,7 @@ def octree_simplify(self, runs=1, plot=False, rotate=True,
             if plot:
                 self.plot()
 
-        vprint('\nReduced to {} points'.format(len(self)))
+        logging.info('\nReduced to {} points'.format(len(self)))
 
     def __len__(self):
         return n.sum(map(len, self.lines))
@@ -426,12 +427,6 @@ def arclength(self, include_closures=True):
         '''
         return n.sum(k.arclength(include_closures) for k in self.lines)
 
-    def _vprint(self, s, newline=True):
-        '''Prints s, with optional newline. Intended for internal use
-        in displaying progress.'''
-        if self.verbose:
-            vprint(s, newline)
-
     def gauss_code(self, **kwargs):
         '''
         Returns a :class:`~pyknotid.representations.gausscode.GaussCode`
@@ -487,5 +482,3 @@ def multivariate_alexander(self, variables=-1., **kwargs):
         gc = self.gauss_code(**kwargs)
         gc.simplify(verbose=self.verbose)
         return multivariate_alexander(gc, variables)
-
-

pyknotid/spacecurves/spacecurve.py

@@ -19,14 +19,15 @@
 
 '''
 
+import logging
 import numpy as n
 import numpy as np
 import sys
 
 try:
     from pyknotid.spacecurves import chelpers
 except ImportError:
-    print('Could not import cythonised chelpers, using Python '
+    logging.warning('Could not import cythonised chelpers, using Python '
           'alternative. This will '
           'give the same result, but is slower.')
     from pyknotid.spacecurves import helpers as chelpers
@@ -133,15 +134,6 @@ def roll(self, distance, fix_endpoints=True):
             points = np.vstack([points, points[:1]])
         self.points = points
 
-    def _vprint(self, s, newline=True):
-        '''Prints s, with optional newline. Intended for internal use
-        in displaying progress.'''
-        if self.verbose:
-            sys.stdout.write(s)
-            if newline:
-                sys.stdout.write('\n')
-            sys.stdout.flush()
-
     def _add_closure(self):
         closing_distance = mag(self.points[-1] - self.points[0])
         if closing_distance > 0.02:
@@ -348,8 +340,8 @@ def from_braid_word(cls, word):
         for i in range(num_strands):
             cur_strand = strands_by_initial_index[index]
             line.extend(cur_strand)
-            print('index is', index)
-            print('cur strand is', cur_strand)
+            logging.info('index is' + str(index))
+            logging.info('cur strand is' + str(cur_strand))
             index = int(np.round(cur_strand[-1][0])) - 1
 
         k = cls(n.array(line)*5.)
@@ -416,7 +408,7 @@ def cuaps(self, include_closure=True):
         tangents = np.roll(points, -1, axis=0) - points
         angles = np.arctan2(tangents[:, 1], tangents[:, 0])
 
-        print('angles', angles)
+        logging.info('angles' + str(angles))
 
         cuaps = []
 
@@ -505,7 +497,7 @@ def raw_crossings(self, mode='use_max_jump', include_closure=True,
         else:
             helpers_module = helpers
 
-        self._vprint('Finding crossings')
+        logging.info('Finding crossings')
 
         points = self.points
         segment_lengths = n.roll(points[:, :2], -1, axis=0) - points[:, :2]
@@ -526,8 +518,7 @@ def raw_crossings(self, mode='use_max_jump', include_closure=True,
         for i in range(len(points)-2):
             if self.verbose:
                 if i % 100 == 0:
-                    self._vprint('\ri = {} / {}'.format(i, numtries),
-                                 False)
+                    logging.info('\ri = {} / {}'.format(i, numtries))
             v0 = points[i]
             dv = points[(i+1) % len(points)] - v0
 
@@ -557,7 +548,7 @@ def raw_crossings(self, mode='use_max_jump', include_closure=True,
                 max_segment_length,
                 jump_mode))
 
-        self._vprint('\n{} crossings found\n'.format(len(crossings) / 2))
+        logging.info('\n{} crossings found\n'.format(len(crossings) / 2))
         crossings.sort(key=lambda s: s[0])
         crossings = n.array(crossings)
         self._crossings = crossings
@@ -714,7 +705,7 @@ def representation(self, recalculate=False, **kwargs):
         gc = Representation(crossings, verbose=self.verbose)
         self._representation = gc
         return gc
-        
+
 
     def planar_diagram(self, **kwargs):
         '''
@@ -840,7 +831,7 @@ def from_csv(cls, filen, **kwargs):
         '''
         Loads knot points from the given csv file, and returns a
         :class:`SpaceCurve` with those points.
-        
+
         Arguments are passed straight to :func:`pyknot.io.from_csv`.
         '''
         return cls(from_csv(filen, **kwargs))
@@ -888,7 +879,7 @@ def octree_simplify(self, runs=1, plot=False, rotate=True,
         from pyknotid.simplify.octree import OctreeCell
         for i in range(runs):
             if len(self.points) > 30:
-                self._vprint('\rRun {} of {}, {} points remain'.format(
+                logging.info('\rRun {} of {}, {} points remain'.format(
                     i, runs, len(self.points)))
 
             if rotate:
@@ -906,7 +897,7 @@ def octree_simplify(self, runs=1, plot=False, rotate=True,
             if plot:
                 self.plot()
 
-        self._vprint('\nReduced to {} points'.format(len(self.points)))
+        logging.info('\nReduced to {} points'.format(len(self.points)))
 
     def arclength(self, include_closure=True):
         '''
@@ -1159,6 +1150,3 @@ def interpolate(self, num_points, s=0, **kwargs):
         new_points[:, 2] = points[2]
 
         self.points = new_points
-
-
-

pyknotid/utils.py

@@ -5,6 +5,7 @@
 
 import sys
 import numpy as n
+import logging
 
 def vprint(string='', newline=True, condition=True):
     '''
@@ -24,10 +25,9 @@ def vprint(string='', newline=True, condition=True):
     '''
     if not condition:
         return
-    sys.stdout.write(string)
     if newline:
-        sys.stdout.write('\n')
-    sys.stdout.flush()
+        string += '\n'
+    logging.info(string)
 
 def mag(v):
     '''
@@ -51,7 +51,7 @@ def get_rotation_matrix(angles):
     angles : iterable
         The psi, theta and phi angles
     '''
-    
+
     phi, theta, psi = angles
     sin = n.sin
     cos = n.cos