Python 3 migration of PyPARIS 2.4.1

Author: giadarol

communication_helpers.py

@@ -6,7 +6,7 @@
 
 def combine_float_buffers(list_of_buffers):
 	N_buffers = len(list_of_buffers)
-	len_buffers = np.array(map(lambda seq: float(len(seq)), list_of_buffers))
+	len_buffers = np.array([float(len(seq)) for seq in list_of_buffers])
 	return np.array(np.concatenate([np.array([float(N_buffers)]), len_buffers]+list_of_buffers),dtype=np.float64)
 
 def split_float_buffers(megabuffer):
@@ -19,7 +19,7 @@ def split_float_buffers(megabuffer):
 	i_mbuf += N_buffers
 
 	list_of_buffers = []
-	for i_buf in xrange(N_buffers):
+	for i_buf in range(N_buffers):
 		lenbuf = int(len_buffers[i_buf])
 		list_of_buffers.append(megabuffer[i_mbuf:i_mbuf+lenbuf])
 		i_mbuf += lenbuf
@@ -31,12 +31,12 @@ def split_float_buffers(megabuffer):
 
 
 def list_of_strings_2_buffer(strlist):
-	data = ''.join(map(lambda s:s+';', strlist))+'\nendbuf\n'
-	buf_to_send = np.atleast_1d(np.int_(np.array(map(ord, list(data)))))
+	data = ''.join([s+';' for s in strlist])+'\nendbuf\n'
+	buf_to_send = np.atleast_1d(np.int_(np.array(list(map(ord, list(data))))))
 	return buf_to_send
 
 def buffer_2_list_of_strings(buf):
-	str_received = ''.join(map(unichr, list(buf)))
+	str_received = ''.join(map(chr, list(buf)))
 	strlist = list(map(str, str_received.split('\nendbuf\n')[0].split(';')))[:-1]
 	return strlist
 
@@ -73,7 +73,7 @@ def beam_2_buffer(beam, mode='pickle', verbose=False):
 		# Beam data buffer
 		if mode=='json':
 			sinfo_str = json.dumps(sinfo)
-			sinfo_int = np.array(map(ord, sinfo_str), dtype=np.int)
+			sinfo_int = np.array(list(map(ord, sinfo_str)), dtype=np.int)
 			sinfo_float_buf = sinfo_int.astype(np.float, casting='safe')
 		elif mode=='pickle':
 			pss = pickle.dumps(sinfo, protocol=2)
@@ -100,10 +100,10 @@ def beam_2_buffer(beam, mode='pickle', verbose=False):
 			np.array([float(len(sinfo_float_buf))]),sinfo_float_buf)), dtype=np.float64)
 
 		if verbose:
-			print('mode=%s'%mode)
-			print('beam.macroparticlenumber:%d'%beam.macroparticlenumber)
-			print('len(buf):%d'%len(buf))
-			print('len(sinfo_float_buf):%d'%len(sinfo_float_buf))
+			print(('mode=%s'%mode))
+			print(('beam.macroparticlenumber:%d'%beam.macroparticlenumber))
+			print(('len(buf):%d'%len(buf)))
+			print(('len(sinfo_float_buf):%d'%len(sinfo_float_buf)))
 
 	return buf
 
@@ -175,7 +175,7 @@ def buffer_2_beam(buf, mode='pickle'):
 
 		if mode=='json':
 			si_int = slice_info_buf.astype(np.int)
-			si_str = ''.join(map(unichr, list(si_int)))
+			si_str = ''.join(map(chr, list(si_int)))
 			beam.slice_info = json.loads(si_str)
 		elif mode=='pickle':
 			# Get length in bytes

gen_multibunch_beam.py

@@ -23,7 +23,7 @@ def gen_matched_multibunch_beam(machine, n_macroparticles_per_bunch, filling_pat
     list_genbunches = []
     for i_slot, inten_slot in enumerate(filling_pattern):
         if inten_slot>0:
-            print('Generating bunch at slot %d/%d'%(i_slot, len(filling_pattern)))
+            print(('Generating bunch at slot %d/%d'%(i_slot, len(filling_pattern))))
             bunch = generate_bunch(n_macroparticles_per_bunch, inten_slot*bunch_intensity, epsn_x, epsn_y, sigma_z=sigma_z)
             bunch.z -= b_spac_buckets*bucket_length_m*i_slot
             list_genbunches.append(bunch)
@@ -63,13 +63,13 @@ def load_multibunch_beam(dirname, reset_i_turns=True):
     import PyPARIS.myfilemanager as mfm
     import PyPARIS.communication_helpers as ch
 
-    print('Loading the beam from %s'%dirname)
+    print(('Loading the beam from %s'%dirname))
 
     bzero = ch.buffer_2_beam(mfm.dict_of_arrays_and_scalar_from_h5(
             dirname+'/bunch0.h5')['bunchbuffer'])
     N_bunches_tot_beam = bzero.slice_info['N_bunches_tot_beam']
     list_bunches = [bzero]
-    for ibun in xrange(1, N_bunches_tot_beam):
+    for ibun in range(1, N_bunches_tot_beam):
         list_bunches.append(ch.buffer_2_beam(
             mfm.dict_of_arrays_and_scalar_from_h5(
             dirname+'/bunch%d.h5'%ibun)['bunchbuffer']))
@@ -89,7 +89,7 @@ def save_bunch_to_folder(bunch, dirname):
         os.makedirs(dirname)
     buf = ch.beam_2_buffer(bunch)
     bpath = dirname+'/bunch%d.h5'%bunch.slice_info['i_bunch']
-    print('Saving: ' + bpath)
+    print(('Saving: ' + bpath))
     mfm.dict_to_h5(dict_save={'bunchbuffer':buf}, 
                    filename=bpath)
 

generate_python3

@@ -3,4 +3,4 @@ rm -rf ../python3/PyPARIS
 cp -r ../PyPARIS ../python3/PyPARIS
 rm ../python3/PyPARIS/*.so
 2to3 --output-dir=../python3/PyPARIS -W -n ../PyPARIS
-rm -rf ../python3/PyPARIS/.git
+# rm -rf ../python3/PyPARIS/.git

multiprocexec.py

@@ -112,7 +112,7 @@ def todo(sim_module_string, pid, N_proc, queue_list,
 
     sim_module_string = sys.argv[3].split('=')[-1]
 
-    queue_list = [mp.Queue() for _ in xrange(N_proc)]
+    queue_list = [mp.Queue() for _ in range(N_proc)]
 
     mutex = mp.Semaphore(1)
     barrier = mp.Semaphore(0)
@@ -121,7 +121,7 @@ def todo(sim_module_string, pid, N_proc, queue_list,
     cnt = mp.Value('i', 0)
 
     proc_list = []
-    for pid in xrange(N_proc):
+    for pid in range(N_proc):
         proc_list.append(mp.Process(target=todo, 
             args=(sim_module_string, pid, N_proc, queue_list,
                     mutex, barrier, turnstile, turnstile2, cnt, multiturn)))

myfilemanager.py

@@ -3,7 +3,7 @@
 
 class obj_from_dict:
     def __init__(self, dictto):
-        for kk in dictto.keys():
+        for kk in list(dictto.keys()):
             setattr(self, kk, dictto[kk])
 
 
@@ -18,7 +18,7 @@ def myloadmat(filename, squeeze = True):
     import scipy.io as sio
     dict_var=sio.loadmat(filename)
     if squeeze:
-        for kk in dict_var.keys():
+        for kk in list(dict_var.keys()):
             try:
                 dict_var[kk]=np.squeeze(dict_var[kk])
             except:
@@ -32,7 +32,7 @@ def dict_of_arrays_and_scalar_from_h5(filename):
     import h5py
     with h5py.File(filename, 'r') as fid:
         f_dict = {}
-        for kk in fid.keys():
+        for kk in list(fid.keys()):
             f_dict[kk] = np.array(fid[kk]).copy()
             if f_dict[kk].shape == ():
                 f_dict[kk] = f_dict[kk].tolist()
@@ -47,7 +47,7 @@ def monitorh5_to_dict(filename, key= 'Bunch'):
     with h5py.File(filename, 'r') as monitor_ev:
         monitor = monitor_ev[key]
         monitor_dict = {}
-        for kk in monitor.keys():
+        for kk in list(monitor.keys()):
             monitor_dict[kk] = np.array(monitor[kk]).copy()
 
     return monitor_dict
@@ -58,15 +58,15 @@ def monitorh5_to_obj(filename, key= 'Bunch'):
 
 def monitorh5list_to_dict(filename_list, key='Bunch', flag_transpose=False, permissive=False):
     monitor_dict = monitorh5_to_dict(filename_list[0], key=key)
-    for i_file in xrange(1, len(filename_list)):
-        print('Loading '+filename_list[i_file])
+    for i_file in range(1, len(filename_list)):
+        print(('Loading '+filename_list[i_file]))
         try:
             monitor_dict_curr = monitorh5_to_dict(filename_list[i_file], key=key)
             if flag_transpose:
-                for kk in monitor_dict.keys():
+                for kk in list(monitor_dict.keys()):
                     monitor_dict[kk] = np.array(list(monitor_dict[kk].T)+list(monitor_dict_curr[kk].T)).T
             else:
-                for kk in monitor_dict.keys():
+                for kk in list(monitor_dict.keys()):
                     monitor_dict[kk] = np.array(list(monitor_dict[kk])+list(monitor_dict_curr[kk]))
         except IOError as err:
             print('Got:')
@@ -83,7 +83,7 @@ def monitorh5list_to_obj(filename_list, key= 'Bunch', flag_transpose=False, perm
 def dict_to_h5(dict_save, filename, compression=None, compression_opts=None):
     import h5py
     with h5py.File(filename, 'w') as fid:
-        for kk in dict_save.keys():
+        for kk in list(dict_save.keys()):
             fid.create_dataset(kk, data=dict_save[kk],
 		compression=compression, compression_opts=compression_opts)
 

ring_of_CPUs.py

@@ -1,10 +1,10 @@
 import numpy as np
 
-import communication_helpers as ch
+from . import communication_helpers as ch
 
 logfilename = 'pyparislog.txt'
 def print2logandstdo(message, mode='a+'):
-    print message
+    print(message)
     with open(logfilename, mode) as fid:
         fid.writelines([message+'\n'])
 
@@ -111,7 +111,7 @@ def run(self):
                 orders_from_master = []
                 list_of_buffers_to_send = []
 
-                for _ in xrange(self.N_pieces_per_transfer):
+                for _ in range(self.N_pieces_per_transfer):
                     # pop a piece
                     try:
                         piece_to_send = self.pieces_to_be_treated.pop() 	# pop starts for the last slices 
@@ -128,7 +128,7 @@ def run(self):
                     raise ValueError('Float buffer is too small!')
                 self.comm.Sendrecv(sendbuf, dest=0, sendtag=0, 
                             recvbuf=self.buf_float, source=self.master_id-1, recvtag=self.myid)
-                list_received_pieces = map(self.sim_content.buffer_to_piece, ch.split_float_buffers(self.buf_float))
+                list_received_pieces = list(map(self.sim_content.buffer_to_piece, ch.split_float_buffers(self.buf_float)))
 
                 # treat received pieces				
                 for piece_received in list_received_pieces:
@@ -187,15 +187,15 @@ def run(self):
                     raise ValueError('Float buffer is too small!')
                 self.comm.Sendrecv(sendbuf, dest=self.right, sendtag=self.right, 
                             recvbuf=self.buf_float, source=self.left, recvtag=self.myid)
-                list_received_pieces = map(self.sim_content.buffer_to_piece, ch.split_float_buffers(self.buf_float))
+                list_received_pieces = list(map(self.sim_content.buffer_to_piece, ch.split_float_buffers(self.buf_float)))
 
                 # treat received piece
                 for piece_received in list_received_pieces:
                     if piece_received is not None:
                         self.sim_content.treat_piece(piece_received) #the elements of the list are being mutated
 
                 # prepare for next iteration
-                list_of_buffers_to_send = map(self.sim_content.piece_to_buffer, list_received_pieces)
+                list_of_buffers_to_send = list(map(self.sim_content.piece_to_buffer, list_received_pieces))
 
                 # receive orders from the master
                 self.comm.Bcast(self.buf_int, self.master_id)
@@ -218,11 +218,11 @@ def run(self):
 
 class SingleCoreComminicator(object):
     def __init__(self):
-        print '\n\n\n'
-        print '****************************************'	
-        print '*** Using single core MPI simulator! ***'	
-        print '****************************************'
-        print '\n\n\n'
+        print('\n\n\n')
+        print('****************************************')	
+        print('*** Using single core MPI simulator! ***')	
+        print('****************************************')
+        print('\n\n\n')
 
     def Get_size(self):
         return 1

ring_of_CPUs_multiturn.py

@@ -3,14 +3,14 @@
 import sys, os
 import socket
 
-from ring_of_CPUs import SingleCoreComminicator
+from .ring_of_CPUs import SingleCoreComminicator
 
-import communication_helpers as ch
+from . import communication_helpers as ch
 from collections import deque
 
 logfilename = 'pyparislog.txt'
 def print2logandstdo(message, mode='a+'):
-    print message
+    print(message)
     with open(logfilename, mode) as fid:
         fid.writelines([message+'\n'])
 
@@ -252,7 +252,7 @@ def run(self):
                     slice_group.append(None)
             else:
                 # Buffer to slice
-                slice_group = map(self.sim_content.buffer_to_piece, list_received_buffers)
+                slice_group = list(map(self.sim_content.buffer_to_piece, list_received_buffers))
 
 
 
@@ -295,7 +295,7 @@ def run(self):
                 list_of_buffers_to_send = [self.sim_content.piece_to_buffer(bunch_to_be_sent)]
             else:
                 # Slice to buffer
-                list_of_buffers_to_send = map(self.sim_content.piece_to_buffer, slice_group)
+                list_of_buffers_to_send = list(map(self.sim_content.piece_to_buffer, slice_group))
 
 
             ########################

slicing_tool.py

@@ -72,12 +72,12 @@ def slice_a_bunch(this_bunch, z_cut, n_slices):
                     mass=this_bunch.mass, circumference=this_bunch.circumference, 
                     gamma=this_bunch.gamma, 
                     coords_n_momenta_dict=this_bunch.get_coords_n_momenta_dict())
-        copy_this_bunch.slice_info = {kk:this_bunch.slice_info[kk] for kk in this_bunch.slice_info.keys()}
+        copy_this_bunch.slice_info = {kk:this_bunch.slice_info[kk] for kk in list(this_bunch.slice_info.keys())}
 
         list_slices_this_bunch = [copy_this_bunch]
 
     for i_sl, ss in enumerate(list_slices_this_bunch[::-1]): # I want slice 0 to be at the head
-        ss.slice_info['info_parent_bunch'] = {kk: this_bunch.slice_info[kk] for kk in this_bunch.slice_info.keys()}
+        ss.slice_info['info_parent_bunch'] = {kk: this_bunch.slice_info[kk] for kk in list(this_bunch.slice_info.keys())}
         ss.slice_info['i_slice'] = i_sl
         ss.slice_info['N_slices_tot_bunch'] = len(list_slices_this_bunch)
 

test_multibunch/000_test_beam_generation/006_test_genbeam_slice_buffer.py

@@ -98,7 +98,7 @@
 # check bunch merge
 list_bunches_rec = []
 for ibun, lbun in enumerate(list_bunch_buffers):
-    list_sl = map(ch.buffer_2_beam, lbun)
+    list_sl = list(map(ch.buffer_2_beam, lbun))
     list_bunches_rec.append(st.merge_slices_into_bunch(list_sl))
 
 fig2 = plt.figure(2, figsize=(8, 6*1.3))

test_multibunch/000_test_beam_generation/machines_for_testing.py

@@ -52,7 +52,7 @@ def __init__(self, machine_configuration=None, optics_mode='smooth', **kwargs):
 
 
         if pp.optics_mode=='smooth':
-            if 's' in kwargs.keys(): raise ValueError('s vector cannot be provided if optics_mode = "smooth"')
+            if 's' in list(kwargs.keys()): raise ValueError('s vector cannot be provided if optics_mode = "smooth"')
 
             pp.n_segments = kwargs['n_segments']
             pp.circumference = 1100*2*np.pi
@@ -65,7 +65,7 @@ def __init__(self, machine_configuration=None, optics_mode='smooth', **kwargs):
             pp.s = None
 
         elif pp.optics_mode=='non-smooth':
-            if 'n_segments' in kwargs.keys(): raise ValueError('n_segments cannot be provided if optics_mode = "non-smooth"')
+            if 'n_segments' in list(kwargs.keys()): raise ValueError('n_segments cannot be provided if optics_mode = "non-smooth"')
             pp.n_segments = None
             pp.circumference = None
 
@@ -100,7 +100,7 @@ def __init__(self, machine_configuration=None, optics_mode='smooth', **kwargs):
         pp.app_y       = 0
         pp.app_xy      = 0
 
-        for attr in kwargs.keys():
+        for attr in list(kwargs.keys()):
             if kwargs[attr] is not None:
                 if type(kwargs[attr]) is list or type(kwargs[attr]) is np.ndarray:
                     str2print = '[%s ...]'%repr(kwargs[attr][0])