def organizar(archivo, folder, destino):
try:
#BLOQUE PARA LA LINEA DE PROGRESO
p = subprocess.Popen(['wc', '-l', archivo], stdout=subprocess.PIPE,stderr=subprocess.PIPE)
result, err = p.communicate()
total_lineas=int(result.strip().split()[0])
number=0
file=open(archivo, 'r')
for linea in file:
#DE LA LINEA OBTIENE LOS TRES PRIMEROS CARACTERES: M16-1578 -> M16
subfolder=linea[:3].lower()
#LINEA DE PROGRESO SE LLAMA EN CADA CICLO
progress.printProgress(number, total_lineas-1, prefix = 'Progress:', suffix = 'Complete', barLength = 50)
number+=1
#SE UNE FODLER DESTINO CON SUBFOLDER. EJEMPLO: PATOLOGIAS/M15
rutaunion=destino+"/"+subfolder
#CONDICION Si NO EXISTE FOLDER EJ: PATOLOG/M16 ENTONCES LO CREA
if not existefolder(rutaunion):
crearfolder(rutaunion)
#VA A COPIAR EJ: (linea)m16-002.txt.html ubicado en (folder)/home/fox copiar hacia (destino)/home/fox/organizado
copiar(linea, folder, rutaunion)
file.close()
print ("\n")
except Exception, e:
print "Ha fallado en organizar",str(e)
sys.exit(1)
def resetProgress(self, printStatus=False):
self.iterationCounter = 0
if printStatus:
printProgress(0, self.maxIterations)
timestep_coords = np.zeros((n_part, 3))
part_id = 0
timestep = 0
print "Read in coordinates..."
for idx, line in enumerate(datafile_numpy):
#skip headerlines plus first timestep line
if idx < n_headerlines + 1:
continue
#search for timestep string
if line == "timestep ordered\n" or line == "t\n":
if timestep % 1000 == 0:
#print "Read in timestep", timestep
printProgress(timestep, n_timesteps)
coords[timestep] = timestep_coords
timestep_coords = np.zeros((n_part, 3))
part_id = 0
timestep += 1
continue
#with correct format this should not happen
if line == "\n":
continue
current_line = line.rstrip()
split_line = current_line.split()
else:
outp=open('../listas_de_vacios/Estan_en_Master_Y_No_VACIOS.txt', 'a')
outp.write(nombre)
outp.write("\n")
outp.close()
out.close()
except Exception, e:
print "Ha fallado",str(e),nombre
sys.exit(1)
if __name__ == '__main__':
p = subprocess.Popen(['wc', '-l', '../listas_de_vacios/NO_estan_en_master.txt'], stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
result, err = p.communicate()
total_lineas=int(result.strip().split()[0])
number=0
lista_vacios=open('../listas_de_vacios/NO_estan_en_master.txt', 'r')
for linea in lista_vacios:
# nombre=str(linea)
# buscarenliliana(linea.strip())
if buscarenliliana(linea.strip()):
None
else:
buscarenerlinda(linea.strip())
progress.printProgress(number, total_lineas-1, prefix = 'Progress:', suffix = 'Complete', barLength = 50)
number+=1
# buscar_en_liliana("m03-6688.txt")
n_frames = coords.shape[0]
n_part = coords.shape[1]
box_l = (n_part * np.pi / (6. * eta))**(1. / 3.)
#indices/ids for different particle types
indices_ptype = {}
vel_distributions = {}
avg_counters = {} #avg_counter[type] = numpy array with length n_bins
for t in list_ptypes:
indices_ptype[t] = np.where(ptypes == t)[0]
vel_distributions[t] = np.zeros(n_bins)
avg_counters[t] = np.zeros(n_bins)
print "Calculate velocity distribution along z axis..."
printProgress(0, n_frames)
for current_frame in xrange(n_frames):
if current_frame == max_frames:
break
for t in list_ptypes:
#z coordinates of interest: np.take(coords[current_frame,:,2], indices_ptype[t])
#velocities of interest (field is applied in x direction): np.take(vels[current_frame,:,0], indices_ptype[t])
current_coords = np.take(coords[current_frame, :, 2], indices_ptype[t])
current_vels = np.take(vels[current_frame, :, 0], indices_ptype[t])
for i in xrange(len(current_vels)):
#bin index is calculates from z coordinate
#bin_idx = int(np.floor(current_coords[i]*n_bins/box_l))
bin_idx = int(np.floor(current_coords[i] % box_l * n_bins / box_l))
counter_particles = 0
#particle_id_deviation = 0 #deviations will be evaluated only for this given particle
particle_id_deviation = n_part - 1 #the last particle is a counterion
coord_part_last_frame = np.array([0., 0., 0.])
dx = np.zeros(n_frames)
for idx, line in enumerate(datafile_countframes):
if idx < n_headerlines:
continue
#starts with first "timestep ordered" or "t" line
if line == "timestep ordered\n" or line == "t\n":
if not counter_frames % 100:
printProgress(counter_frames, n_frames)
if counter_particles != n_part and counter_frames:
validity_buffer += "Frame {0} corrupt: found only {1}/{2} particles.\n".format(
counter_frames, counter_particles, n_part)
counter_particles = 0
counter_frames += 1
elif line == "\n":
continue
else:
#should find only coordinates
current_line = line.rstrip()
split_line = current_line.split()
try:
coords = np.zeros((n_timesteps, n_part, 3))
timestep_coords = np.zeros((n_part, 3))
part_id = 0
timestep = 0
for idx, line in enumerate(datafile_numpy):
#skip headerlines plus first timestep line
if idx < n_headerlines+1:
continue
#search for timestep string
if line == "timestep ordered\n" or line =="t\n":
if timestep%100==0:
#print "Read in timestep", timestep
printProgress(timestep, n_timesteps)
coords[timestep] = timestep_coords
timestep_coords = np.zeros((n_part, 3))
part_id = 0
timestep += 1
continue
#with correct format this should not happen
if line == "\n":
continue
current_line = line.rstrip()
split_line = current_line.split()