def __generate_movie__(movie_specification):
"""
function generate a movie using mencoder based on frame's files extension
or a file listing
"""
m = movie_specification
if m.idx == None:
output_file = as_path(m.directory, '%s.avi' % (m.name))
else:
output_file = as_path(m.directory,
'%s_part_%02i.avi' % (m.name, m.idx))
#frames_file if not null contains frames listing
frames_source = 'mf://' + (('@' + m.frames_file) if m.frames_file else
as_path(m.movie_directory, m.movie_frames))
command = ('mencoder',
frames_source,
#'mf://@' + m.frames_file,
'-mf',
#'type=png:w=1024:h=800:fps=30',
'type=png:w=' + str(m.width) + \
':h=' + str(m.height) + \
':fps=' + str(m.fps),
'-ovc',
'lavc',
'-lavcopts',
'vcodec=mpeg4:mbd=2:trell',
'-oac',
'copy',
'-o',
'%s' % (output_file))
os.spawnvp(os.P_WAIT, 'mencoder', command)
return output_file
def __generate_movie__(movie_specification):
"""
function generate a movie using mencoder based on frame's files extension
or a file listing
"""
m = movie_specification
if m.idx == None:
output_file = as_path(m.directory, '%s.avi' % (m.name))
else:
output_file = as_path(m.directory,
'%s_part_%02i.avi' % (m.name, m.idx))
#frames_file if not null contains frames listing
frames_source = 'mf://' + (('@' + m.frames_file)
if m.frames_file else as_path(m.movie_directory, m.movie_frames))
command = ('mencoder',
frames_source,
#'mf://@' + m.frames_file,
'-mf',
#'type=png:w=1024:h=800:fps=30',
'type=png:w=' + str(m.width) + \
':h=' + str(m.height) + \
':fps=' + str(m.fps),
'-ovc',
'lavc',
'-lavcopts',
'vcodec=mpeg4:mbd=2:trell',
'-oac',
'copy',
'-o',
'%s' % (output_file))
os.spawnvp(os.P_WAIT, 'mencoder', command)
return output_file
def __init__(self, pp_specs_manager):
super(PoincarePlotAnimation, self).__init__(pp_specs_manager)
interval = int(1000.0 / self.manager.movie_fps)
ani = animation.FuncAnimation(self.fig,
self.update_plot,
init_func=self.setup_plot,
frames=len(self.pp_specs),
interval=interval,
blit=True,
repeat_delay=0,
repeat=False)
p0 = self.pp_specs[0] # alias
output_movie_file = as_path(
self.manager.movie_dir,
'%s_%06d.mp4' % (self.manager.movie_name, p0.idx))
ani.save(
output_movie_file,
fps=self.manager.movie_fps,
dpi=self.manager.movie_dpi,
#extra_args=['-vcodec', 'libx264']
#extra_args=['-vcodec', 'mpeg4']
#extra_args=['-vcodec', 'h264']
#, '-lavcopts', 'vcodec=avi']
)
def save_movie(self):
if not self.__prefixed_movie_name__ == None and self.p.movie_not_save == False: # @IgnorePep8
output_file = generate_movie(self.__prefixed_movie_name__,
self.__prefixed_movie_dir__,
self.p.movie_width, self.p.movie_height,
self.p.movie_fps,
movie_clean_frames=self.p.movie_clean_frames)
self.message = "Poincare plot movie %s is created !" \
% as_path(self.__prefixed_movie_dir__, output_file)
def __get_prefixed_movie_dir__(self):
"""
method returns prefixed movie_dir by source name and output_prefix
"""
movie_dir = self.p.movie_dir
prefix = self.p.output_prefix + '_' \
if not is_empty(self.p.output_prefix) else ''
return as_path(movie_dir, prefix + 'm_' + self.source) \
if self.p.movie_prefixed_by_source else movie_dir
def __get_prefixed_movie_dir__(self):
"""
method returns prefixed movie_dir by source name and output_prefix
"""
movie_dir = self.p.movie_dir
prefix = self.p.output_prefix + '_' \
if not is_empty(self.p.output_prefix) else ''
return as_path(movie_dir, prefix + 'm_' + self.source) \
if self.p.movie_prefixed_by_source else movie_dir
def save_movie(self):
if not self.__prefixed_movie_name__ == None and self.p.movie_not_save == False: # @IgnorePep8
output_file = generate_movie(
self.__prefixed_movie_name__,
self.__prefixed_movie_dir__,
self.p.movie_width,
self.p.movie_height,
self.p.movie_fps,
movie_clean_frames=self.p.movie_clean_frames)
self.message = "Poincare plot movie %s is created !" \
% as_path(self.__prefixed_movie_dir__, output_file)
def __save_members__(self):
"""
[optional]
save members values
"""
if self.save_parameters:
_filename = as_path(self.output_dir, "pp_parameters.txt")
create_dir(self.output_dir)
with open(_filename, 'w') as _file:
for info_line in self.__p__.get_infos_lines(valued_only=True):
_file.write(info_line + "\n")
print('Poincare plot parameters saved into a file: %s ' %
(_filename))
def __save_members__(self):
"""
[optional]
save members values
"""
if self.save_parameters:
_filename = as_path(self.output_dir, "pp_parameters.txt")
create_dir(self.output_dir)
with open(_filename, 'w') as _file:
for info_line in self.__p__.get_infos_lines(valued_only=True):
_file.write(info_line + "\n")
print('Poincare plot parameters saved into a file: %s '
% (_filename))
def __process__(self, _file_handler, disp=True, **params):
"""
the method which starts to generate Poincare Plot parameters
"""
sign_multiplicator = 80
file_counter = 0
if disp:
print('*' * sign_multiplicator)
if self.group_data_filename and self.data_file == None:
#create a group data input file
outfilename = as_path(self.output_dir,
"grp_" + self.group_data_filename)
joined = join_files(self.__data_filenames__(),
headers_count=self.headers_count,
outfilename=outfilename)
if joined:
self.data_file = outfilename
if disp:
print('Using group data file: ' + self.data_file)
if self.data_file: # data_file parameter is superior to data_dir parameter @IgnorePep8
_data_file = self.__shuffle_file__(self.data_file)
if os.path.exists(_data_file) == False:
if disp:
print('The file: ' + _data_file + " doesn't exist")
else:
file_counter = 1
if self.__p__.check_data_indexes(_data_file, disp):
_file_handler(_data_file, disp=disp, **params)
else:
for _file in self.__data_filenames__():
if os.path.isfile(_file):
file_counter = file_counter + 1
if disp:
print('=' * sign_multiplicator)
if not self.__p__.check_data_indexes(_file, disp):
continue
if _file_handler(_file, disp=disp, **params) == False:
break
if disp:
print('Processing finished')
if file_counter == 0:
print('No files to process [' + self.data_dir
+ self.extension + ']')
else:
print('Number of processed files: ' + str(file_counter))
def __process__(self, _file_handler, disp=True, **params):
"""
the method which starts to generate Poincare Plot parameters
"""
sign_multiplicator = 80
file_counter = 0
if disp:
print('*' * sign_multiplicator)
if self.group_data_filename and self.data_file == None:
#create a group data input file
outfilename = as_path(self.output_dir,
"grp_" + self.group_data_filename)
joined = join_files(self.__data_filenames__(),
headers_count=self.headers_count,
outfilename=outfilename)
if joined:
self.data_file = outfilename
if disp:
print('Using group data file: ' + self.data_file)
if self.data_file: # data_file parameter is superior to data_dir parameter @IgnorePep8
_data_file = self.__shuffle_file__(self.data_file)
if os.path.exists(_data_file) == False:
if disp:
print('The file: ' + _data_file + " doesn't exist")
else:
file_counter = 1
if self.__p__.check_data_indexes(_data_file, disp):
_file_handler(_data_file, disp=disp, **params)
else:
for _file in self.__data_filenames__():
if os.path.isfile(_file):
file_counter = file_counter + 1
if disp:
print('=' * sign_multiplicator)
if not self.__p__.check_data_indexes(_file, disp):
continue
if _file_handler(_file, disp=disp, **params) == False:
break
if disp:
print('Processing finished')
if file_counter == 0:
print('No files to process [' + self.data_dir +
self.extension + ']')
else:
print('Number of processed files: ' + str(file_counter))
def create_many_plots(_source_file, headers, separator, window_size=None):
"""
draws many plots base on data from _source_file and collection of headers
grouped by a semicolon, elements in a group are separated by a comma
"""
colors = ['red', 'green', 'blue', 'yellow', 'black', 'cyan', 'magenta']
first_line = get_first_lines(_source_file)
if len(first_line) == 0:
return
file_headers = [
header.strip().lower() for header in first_line[0].split(separator)
]
for sub_headers in get_as_list(headers, separator=';'):
labels = [label.strip().lower() for label in get_as_list(sub_headers)]
try:
cols = tuple([file_headers.index(label) for label in labels])
except ValueError:
continue
if separator == None:
values = np.loadtxt(_source_file,
skiprows=1,
unpack=True,
usecols=cols)
else:
values = np.loadtxt(_source_file,
skiprows=1,
unpack=True,
usecols=cols,
delimiter=separator)
plt.gca().set_color_cycle(colors[:len(labels)])
filename = get_filename(_source_file)
title = "%s %s" % (filename, nvl(window_size + " window size", ''))
plt.title(title)
for value in values:
plt.plot(value)
plt.legend(labels, loc='upper right')
plt.axes().set_xlabel('Time')
plot_filename = "%s_%s.png" % (filename, '_'.join(labels))
_file = as_path(fs.dirname(_source_file), plot_filename)
plt.savefig(_file)
plt.cla()
def create_many_plots(_source_file, headers, separator, window_size=None):
"""
draws many plots base on data from _source_file and collection of headers
grouped by a semicolon, elements in a group are separated by a comma
"""
colors = ['red', 'green', 'blue', 'yellow', 'black', 'cyan', 'magenta']
first_line = get_first_lines(_source_file)
if len(first_line) == 0:
return
file_headers = [header.strip().lower()
for header in first_line[0].split(separator)]
for sub_headers in get_as_list(headers, separator=';'):
labels = [label.strip().lower()
for label in get_as_list(sub_headers)]
try:
cols = tuple([file_headers.index(label) for label in labels])
except ValueError:
continue
if separator == None:
values = np.loadtxt(_source_file, skiprows=1, unpack=True,
usecols=cols)
else:
values = np.loadtxt(_source_file, skiprows=1, unpack=True,
usecols=cols, delimiter=separator)
plt.gca().set_color_cycle(colors[:len(labels)])
filename = get_filename(_source_file)
title = "%s %s" % (filename, nvl(window_size + " window size", ''))
plt.title(title)
for value in values:
plt.plot(value)
plt.legend(labels, loc='upper right')
plt.axes().set_xlabel('Time')
plot_filename = "%s_%s.png" % (filename, '_'.join(labels))
_file = as_path(fs.dirname(_source_file), plot_filename)
plt.savefig(_file)
plt.cla()
def __init__(self, pp_specs_manager):
super(PoincarePlotAnimation, self).__init__(pp_specs_manager)
interval = int(1000.0 / self.manager.movie_fps)
ani = animation.FuncAnimation(self.fig,
self.update_plot,
init_func=self.setup_plot,
frames=len(self.pp_specs),
interval=interval,
blit=True,
repeat_delay=0,
repeat=False)
p0 = self.pp_specs[0] # alias
output_movie_file = as_path(self.manager.movie_dir,
'%s_%06d.mp4' % (self.manager.movie_name, p0.idx))
ani.save(output_movie_file, fps=self.manager.movie_fps,
dpi=self.manager.movie_dpi,
#extra_args=['-vcodec', 'libx264']
#extra_args=['-vcodec', 'mpeg4']
#extra_args=['-vcodec', 'h264']
#, '-lavcopts', 'vcodec=avi']
)
from hra_core.io_utils import as_path
import hra_math.time_domain.poincare_plot.poincare_plot as poincare
root_dir = '/home/jurek/volumes/doctoral/monitor_do_impedancji_niccomo/'
result_dir = 'results'
groups = ['_healthy', '_team']
#groups = ['_healthy']
parameters = ['SV', 'SVR', 'CO', 'PEP', 'LVET']
#parameters = ['SV']
types = ['sliding', 'jumping']
for group in groups:
for parameter in parameters:
for _type in types:
base_output_dir = as_path(root_dir, result_dir, group, _type) + fs.sep # @IgnorePep8
#parameters
parameter_dir = as_path(base_output_dir, parameter) + fs.sep
pp = poincare.PoincarePlotManager()
pp.window_size = '5m'
#pp.data_file = as_path(root_dir, group, '001.res')
pp.data_dir = as_path(root_dir, group) + fs.sep
pp.output_dir = parameter_dir
pp.signal_label = parameter
pp.time_label = 'time'
pp.extension = '*.res'
pp.statistics_names = 'c1d, c1a, c2d, c2a, cd, ca, asymmetry'
pp.output_separator = '; '
pp.override_existing_outcomes = True
pp.headers_count = 2
def __generate_multiprocessing_movie__(movie_name, movie_dir, movie_width,
movie_height, movie_fps, movie_frames,
movie_clean_frames):
"""
generating a movie with given specification using multiprocessing;
all frames are divided into excluded sets of files, for each set
a movie is create, in the next step all parts are joined to create
one final movie
"""
#delete previous partial listing files
command = 'rm %s' % as_path(movie_dir, '%s_lst_*' % (movie_name))
execute_command(command)
#create listing of all files
listing_file = str(as_path(movie_dir, movie_name + ".lst"))
#command = 'ls %s > %s' % (as_path(movie_dir, movie_frames), listing_file)
#a better version with no trouble with a limit of number of files of ls command
command = '(cd %s; find $PWD -name \'*.png\' | sort > %s)' % (movie_dir,
listing_file)
execute_command(command)
#get number of movie frames
command = 'wc -l %s' % listing_file
count = int(execute_command(command, 1).split()[0])
#get bytes per line
command = 'head %s' % listing_file
bytes_per_line = int(len(execute_command(command, 1)))
#divide number of files frames per processors count
size = count / multiprocessing.cpu_count()
#split listing file into equal parts prefixed <movie_name>_lst_
command = '(cd %s; split -C %i %s %s_lst_)' % \
(movie_dir, bytes_per_line * size, listing_file, movie_name)
execute_command(command)
#delete all previous movie parts
command = 'rm %s' % as_path(movie_dir, '%s_part_*.avi' % (movie_name))
execute_command(command)
movie_specifications = []
#iterate over splits to create movie_specifications objects
command = 'ls ' + as_path(movie_dir, '%s_lst_*' % (movie_name))
for idx, frames_file in enumerate(run_command(command)):
frames_file = frames_file.replace('\n', '')
movie_specification = MovieSpecification(movie_name, movie_dir,
movie_width, movie_height,
movie_fps, frames_file, idx,
movie_frames)
movie_specifications.append(movie_specification)
#run generation of partial movies
pool = multiprocessing.Pool(processes=multiprocessing.cpu_count())
#if not self.params.info_message_handler == None:
# self.params.info_message_handler('Generating frames'
# + (' ' * 20))
pool.map(__generate_movie__, movie_specifications)
pool.close()
#join all video part movies
movie_draft = movie_name + '_draft.avi'
command = '(cd %s; cat %s_part_*.avi > %s)' % (movie_dir, movie_name,
movie_draft)
execute_command(command)
#convert draft file into final movie file
output_file = '%s.avi' % (movie_name)
command = '(cd %s; mencoder %s -o %s -forceidx -ovc copy -oac copy)' \
% (movie_dir, movie_draft, output_file)
execute_command(command)
#delete draft movie
command = 'rm %s' % as_path(movie_dir, movie_draft)
execute_command(command)
#delete all movie parts
command = 'rm %s' % as_path(movie_dir, '%s_part_*.avi' % (movie_name))
execute_command(command)
#delete partial listing files
command = 'rm %s' % as_path(movie_dir, '%s_lst_*' % (movie_name))
execute_command(command)
# delete frames files
if movie_clean_frames:
command = 'cat %s | xargs rm ' % as_path(movie_dir, '%s.lst' %
(movie_name))
execute_command(command)
#delete listing of all files
command = 'rm %s' % as_path(movie_dir, '%s.lst' % (movie_name))
execute_command(command)
return output_file
def add_data_vector_segment(self, data_vector_segment, last_segment=False):
self.message = None
if self.__prefixed_movie_name__ == None:
return
if last_segment:
self.__save_frames__()
return
frame_name = '%s_%06d' % (self.__prefixed_movie_name__, self.idx)
frame_file = as_path(self.__prefixed_movie_dir__, frame_name + '.png')
#skip_frame = True if self.idx < self.p.movie_skip_to_frame or \
# (self.p.movie_skip_frames and os.path.exists(frame_file)) \
# else False
skip_frame = False
mean_plus = pl.mean(data_vector_segment.signal_plus)
mean_minus = pl.mean(data_vector_segment.signal_minus)
s_plus = len(data_vector_segment.signal_plus)
_pp_spec = MiniPoincarePlotSpec()
_pp_spec.idx = self.idx
_pp_spec.s_plus = s_plus
_pp_spec.mean_plus = mean_plus
_pp_spec.mean_minus = mean_minus
_pp_spec.range = self.range
_pp_spec.frame_file = frame_file
if self.idx == 0:
self.s_size = s_plus
self.x_data.put(pl.arange(s_plus), data_vector_segment.signal_plus)
self.y_data.put(pl.arange(s_plus),
data_vector_segment.signal_minus)
ok = True
old_s_plus = 0
_pp_spec.level = 0
_pp_spec.active_start = 0
_pp_spec.active_stop = s_plus
else:
old_s_plus = len(self.old_signal_plus)
ok = False
if s_plus >= old_s_plus:
if pl.all(self.old_signal_plus \
== data_vector_segment.signal_plus[:old_s_plus]):
old_size = self.s_size
new_size = old_size + s_plus - old_s_plus
if new_size > old_size:
_pp_spec.active_start = old_size
_pp_spec.active_stop = new_size
if new_size > len(self.x_data):
raise Exception(
'New size is greater then the signal size !')
self.x_data.put(
pl.arange(old_size, new_size),
data_vector_segment.signal_plus[old_s_plus -
s_plus:])
self.y_data.put(
pl.arange(old_size, new_size),
data_vector_segment.signal_minus[old_s_plus -
s_plus:])
_pp_spec.inactive_stop = \
self._pp_spec_old.inactive_stop
self.s_size = new_size
_pp_spec.level = 1
ok = True
else:
for idx in xrange(1, old_s_plus):
if pl.all(self.old_signal_plus[idx:] \
== data_vector_segment.signal_plus[idx - 1:
old_s_plus - idx]):
old_size = self.s_size
new_size = old_size + s_plus - (old_s_plus - idx)
if new_size > len(self.x_data):
raise Exception(
'New size is greater then the signal size !'
)
if new_size > old_size:
_pp_spec.active_start = old_size
_pp_spec.active_stop = new_size
self.x_data.put(
pl.arange(old_size,
new_size), data_vector_segment.
signal_plus[old_s_plus - idx:])
self.y_data.put(
pl.arange(old_size,
new_size), data_vector_segment.
signal_minus[old_s_plus - idx:])
self.s_size = new_size
_d = self.s_size - s_plus
_pp_spec.inactive_start = _d - idx
_pp_spec.inactive_stop = _d
_pp_spec.level = 3
ok = True
break
else:
for idx in xrange(1, old_s_plus):
if idx + s_plus <= old_s_plus \
and pl.all(
self.old_signal_plus[idx:idx + s_plus] \
== data_vector_segment.signal_plus):
_d = self.s_size - old_s_plus
_pp_spec.inactive_start = _d
_pp_spec.inactive_stop = _d + idx
if _pp_spec.inactive_stop + s_plus < self.s_size:
_pp_spec.inactive_start_2 = \
_pp_spec.inactive_stop + s_plus
_pp_spec.inactive_stop_2 = self.s_size
_pp_spec.level = 2
ok = True
break
if ok == True and skip_frame == False:
_pp_spec.x_data = self.x_data
_pp_spec.y_data = self.y_data
_pp_spec.cum_inactive = self.cum_inactive
_pp_spec.s_size = self.s_size
#print('PP_SPEC: ' + str(_p))
self.pp_spec_manager.addMiniPoincarePlotSpec(_pp_spec)
if self.idx > 0 and \
(self.p.movie_bin_size > 0
and ((self.idx % self.p.movie_bin_size) == 0)):
if len(self.pp_specs_managers) >= self.core_nums:
if self.p.movie_calculate_all_frames == False:
self.__save_frames__()
self.pp_specs_managers = []
old_pp_spec_manager = self.pp_spec_manager
self.pp_spec_manager = MiniPoincarePlotSpecManager()
self.pp_spec_manager.movie_dir = self.__prefixed_movie_dir__
self.pp_spec_manager.movie_name = self.__prefixed_movie_name__
self.pp_spec_manager.movie_dpi = self.p.movie_dpi
self.pp_spec_manager.movie_fps = self.p.movie_fps
self.pp_spec_manager.movie_height = self.p.movie_height
self.pp_spec_manager.movie_width = self.p.movie_width
self.pp_spec_manager.active_color = self.active_color
self.pp_spec_manager.inactive_color = self.inactive_color
self.pp_spec_manager.centroid_color = self.centroid_color
self.pp_spec_manager.active_point_size = \
self.p.movie_active_size
self.pp_spec_manager.inactive_point_size = \
self.p.movie_inactive_size
self.pp_spec_manager.centroid_point_size = \
self.p.movie_centroid_size
self.pp_spec_manager.show_plot_legends = \
self.p.movie_show_plot_legends
self.pp_spec_manager.x_label = self.p.x_label
self.pp_spec_manager.y_label = self.p.y_label
self.pp_spec_manager.clean_frames = self.p.movie_clean_frames
self.pp_spec_manager.movie_title = self.p.movie_title
self.pp_spec_manager.movie_frame_step = self.p.movie_frame_step
self.pp_spec_manager.movie_identity_line = self.p.movie_identity_line
self.pp_spec_manager.movie_hour_label = self.p.movie_hour_label
self.pp_spec_manager.movie_minute_label = self.p.movie_minute_label
self.pp_spec_manager.movie_second_label = self.p.movie_second_label
self.pp_spec_manager.movie_time_label_in_line = self.p.movie_time_label_in_line
self.pp_spec_manager.movie_time_label_font_size = self.p.movie_time_label_font_size
self.pp_spec_manager.movie_time_label_prefix = self.p.movie_time_label_prefix
self.pp_spec_manager.movie_title_font_size = self.p.movie_title_font_size
self.pp_spec_manager.movie_axis_font_size = self.p.movie_axis_font_size
self.pp_spec_manager.movie_axis_font = self.p.movie_axis_font
self.pp_spec_manager.movie_title_font = self.p.movie_title_font
self.pp_spec_manager.movie_tick_font = self.p.movie_tick_font
self.pp_spec_manager.movie_frame_pad = self.p.movie_frame_pad
self.pp_spec_manager.movie_create_time_label = self.p.movie_create_time_label
self.pp_spec_manager.movie_frame_filename_with_time = self.p.movie_frame_filename_with_time
#add all previous pp specs
for pp_spec in old_pp_spec_manager.getMiniPoincarePlotSpecs():
self.pp_spec_manager.addPreviousPoincarePlotSpecMinimum(
pp_spec)
old_pp_spec_manager = None
self.pp_specs_managers.append(self.pp_spec_manager)
self.message = 'Prepare frame: %s' % (frame_name)
elif ok == True and skip_frame == True:
self.message = 'Skip frame %s' % (frame_name)
elif ok == False:
print('s_plus: ' + str(s_plus) + ' old_s_plus: ' + str(old_s_plus))
print('old_signal_plus: ' + str(self.old_signal_plus))
print('signal_plus: ' + str(data_vector_segment.signal_plus))
raise Exception('Error for idx ' + str(self.idx))
if _pp_spec.inactive_start >= 0 and _pp_spec.inactive_stop >= 0:
#if time array is not None use it as array for cumulative time
if not self.time == None:
self.cum_inactive += pl.sum(
self.time[_pp_spec.inactive_start:_pp_spec.inactive_stop])
else:
self.cum_inactive += pl.sum(
self.x_data[_pp_spec.inactive_start:_pp_spec.
inactive_stop])
self.old_signal_plus = data_vector_segment.signal_plus
self.idx = self.idx + 1
self._pp_spec_old = _pp_spec
root_dir = '/home/jurek/volumes/doctoral/monitor_do_impedancji_niccomo/'
result_dir = 'results_whole_for_R'
groups = ['_healthy', '_team']
#groups = ['_healthy']
parameters = ['SV', 'SVR', 'CO', 'PEP', 'LVET']
#parameters = ['SV']
#types = ['sliding', 'jumping']
#types = ['jumping']
types = ['whole']
for group in groups:
for parameter in parameters:
for _type in types:
base_output_dir = as_path(root_dir, result_dir, group, _type) + fs.sep # @IgnorePep8
#parameters
parameter_dir = as_path(base_output_dir, parameter) + fs.sep
pp = poincare.PoincarePlotManager()
#if not _type == None:
#pp.window_size = '5m'
#pp.data_file = as_path(root_dir, group, '001.res')
pp.data_dir = as_path(root_dir, group) + fs.sep
pp.output_dir = parameter_dir
pp.signal_label = parameter
pp.time_label = 'time'
pp.extension = '*.res'
pp.statistics_names = 'sd1, sd2, sd1d, sd1a, sd2d, sd2a, sdnnd, sdnna, sdnn, c1d, c1a, c2a, c2d, ca, cd' # @IgnorePep8
pp.output_separator = '; '
pp.override_existing_outcomes = True
root_dir = '/home/jurek/volumes/doctoral/monitor_do_impedancji_niccomo/'
result_dir = 'results_whole_for_R'
groups = ['_healthy', '_team']
#groups = ['_healthy']
parameters = ['SV', 'SVR', 'CO', 'PEP', 'LVET']
#parameters = ['SV']
#types = ['sliding', 'jumping']
#types = ['jumping']
types = ['whole']
for group in groups:
for parameter in parameters:
for _type in types:
base_output_dir = as_path(root_dir, result_dir, group,
_type) + fs.sep # @IgnorePep8
#parameters
parameter_dir = as_path(base_output_dir, parameter) + fs.sep
pp = poincare.PoincarePlotManager()
#if not _type == None:
#pp.window_size = '5m'
#pp.data_file = as_path(root_dir, group, '001.res')
pp.data_dir = as_path(root_dir, group) + fs.sep
pp.output_dir = parameter_dir
pp.signal_label = parameter
pp.time_label = 'time'
pp.extension = '*.res'
pp.statistics_names = 'sd1, sd2, sd1d, sd1a, sd2d, sd2a, sdnnd, sdnna, sdnn, c1d, c1a, c2a, c2d, ca, cd' # @IgnorePep8
pp.output_separator = '; '
pp.override_existing_outcomes = True
def add_data_vector_segment(self, data_vector_segment, last_segment=False):
self.message = None
if self.__prefixed_movie_name__ == None:
return
if last_segment:
self.__save_frames__()
return
frame_name = '%s_%06d' % (self.__prefixed_movie_name__, self.idx)
frame_file = as_path(self.__prefixed_movie_dir__, frame_name + '.png')
#skip_frame = True if self.idx < self.p.movie_skip_to_frame or \
# (self.p.movie_skip_frames and os.path.exists(frame_file)) \
# else False
skip_frame = False
mean_plus = pl.mean(data_vector_segment.signal_plus)
mean_minus = pl.mean(data_vector_segment.signal_minus)
s_plus = len(data_vector_segment.signal_plus)
_pp_spec = MiniPoincarePlotSpec()
_pp_spec.idx = self.idx
_pp_spec.s_plus = s_plus
_pp_spec.mean_plus = mean_plus
_pp_spec.mean_minus = mean_minus
_pp_spec.range = self.range
_pp_spec.frame_file = frame_file
if self.idx == 0:
self.s_size = s_plus
self.x_data.put(pl.arange(s_plus), data_vector_segment.signal_plus)
self.y_data.put(pl.arange(s_plus),
data_vector_segment.signal_minus)
ok = True
old_s_plus = 0
_pp_spec.level = 0
_pp_spec.active_start = 0
_pp_spec.active_stop = s_plus
else:
old_s_plus = len(self.old_signal_plus)
ok = False
if s_plus >= old_s_plus:
if pl.all(self.old_signal_plus \
== data_vector_segment.signal_plus[:old_s_plus]):
old_size = self.s_size
new_size = old_size + s_plus - old_s_plus
if new_size > old_size:
_pp_spec.active_start = old_size
_pp_spec.active_stop = new_size
if new_size > len(self.x_data):
raise Exception(
'New size is greater then the signal size !')
self.x_data.put(pl.arange(old_size, new_size),
data_vector_segment.signal_plus[old_s_plus
- s_plus:])
self.y_data.put(pl.arange(old_size, new_size),
data_vector_segment.signal_minus[old_s_plus
- s_plus:])
_pp_spec.inactive_stop = \
self._pp_spec_old.inactive_stop
self.s_size = new_size
_pp_spec.level = 1
ok = True
else:
for idx in xrange(1, old_s_plus):
if pl.all(self.old_signal_plus[idx:] \
== data_vector_segment.signal_plus[idx - 1:
old_s_plus - idx]):
old_size = self.s_size
new_size = old_size + s_plus - (old_s_plus - idx)
if new_size > len(self.x_data):
raise Exception(
'New size is greater then the signal size !')
if new_size > old_size:
_pp_spec.active_start = old_size
_pp_spec.active_stop = new_size
self.x_data.put(pl.arange(old_size, new_size),
data_vector_segment.signal_plus[
old_s_plus - idx:])
self.y_data.put(pl.arange(old_size, new_size),
data_vector_segment.signal_minus[
old_s_plus - idx:])
self.s_size = new_size
_d = self.s_size - s_plus
_pp_spec.inactive_start = _d - idx
_pp_spec.inactive_stop = _d
_pp_spec.level = 3
ok = True
break
else:
for idx in xrange(1, old_s_plus):
if idx + s_plus <= old_s_plus \
and pl.all(
self.old_signal_plus[idx:idx + s_plus] \
== data_vector_segment.signal_plus):
_d = self.s_size - old_s_plus
_pp_spec.inactive_start = _d
_pp_spec.inactive_stop = _d + idx
if _pp_spec.inactive_stop + s_plus < self.s_size:
_pp_spec.inactive_start_2 = \
_pp_spec.inactive_stop + s_plus
_pp_spec.inactive_stop_2 = self.s_size
_pp_spec.level = 2
ok = True
break
if ok == True and skip_frame == False:
_pp_spec.x_data = self.x_data
_pp_spec.y_data = self.y_data
_pp_spec.cum_inactive = self.cum_inactive
_pp_spec.s_size = self.s_size
#print('PP_SPEC: ' + str(_p))
self.pp_spec_manager.addMiniPoincarePlotSpec(_pp_spec)
if self.idx > 0 and \
(self.p.movie_bin_size > 0
and ((self.idx % self.p.movie_bin_size) == 0)):
if len(self.pp_specs_managers) >= self.core_nums:
if self.p.movie_calculate_all_frames == False:
self.__save_frames__()
self.pp_specs_managers = []
old_pp_spec_manager = self.pp_spec_manager
self.pp_spec_manager = MiniPoincarePlotSpecManager()
self.pp_spec_manager.movie_dir = self.__prefixed_movie_dir__
self.pp_spec_manager.movie_name = self.__prefixed_movie_name__
self.pp_spec_manager.movie_dpi = self.p.movie_dpi
self.pp_spec_manager.movie_fps = self.p.movie_fps
self.pp_spec_manager.movie_height = self.p.movie_height
self.pp_spec_manager.movie_width = self.p.movie_width
self.pp_spec_manager.active_color = self.active_color
self.pp_spec_manager.inactive_color = self.inactive_color
self.pp_spec_manager.centroid_color = self.centroid_color
self.pp_spec_manager.active_point_size = \
self.p.movie_active_size
self.pp_spec_manager.inactive_point_size = \
self.p.movie_inactive_size
self.pp_spec_manager.centroid_point_size = \
self.p.movie_centroid_size
self.pp_spec_manager.show_plot_legends = \
self.p.movie_show_plot_legends
self.pp_spec_manager.x_label = self.p.x_label
self.pp_spec_manager.y_label = self.p.y_label
self.pp_spec_manager.clean_frames = self.p.movie_clean_frames
self.pp_spec_manager.movie_title = self.p.movie_title
self.pp_spec_manager.movie_frame_step = self.p.movie_frame_step
self.pp_spec_manager.movie_identity_line = self.p.movie_identity_line
self.pp_spec_manager.movie_hour_label = self.p.movie_hour_label
self.pp_spec_manager.movie_minute_label = self.p.movie_minute_label
self.pp_spec_manager.movie_second_label = self.p.movie_second_label
self.pp_spec_manager.movie_time_label_in_line = self.p.movie_time_label_in_line
self.pp_spec_manager.movie_time_label_font_size = self.p.movie_time_label_font_size
self.pp_spec_manager.movie_time_label_prefix = self.p.movie_time_label_prefix
self.pp_spec_manager.movie_title_font_size = self.p.movie_title_font_size
self.pp_spec_manager.movie_axis_font_size = self.p.movie_axis_font_size
self.pp_spec_manager.movie_axis_font = self.p.movie_axis_font
self.pp_spec_manager.movie_title_font = self.p.movie_title_font
self.pp_spec_manager.movie_tick_font = self.p.movie_tick_font
self.pp_spec_manager.movie_frame_pad = self.p.movie_frame_pad
self.pp_spec_manager.movie_create_time_label = self.p.movie_create_time_label
self.pp_spec_manager.movie_frame_filename_with_time = self.p.movie_frame_filename_with_time
#add all previous pp specs
for pp_spec in old_pp_spec_manager.getMiniPoincarePlotSpecs():
self.pp_spec_manager.addPreviousPoincarePlotSpecMinimum(
pp_spec)
old_pp_spec_manager = None
self.pp_specs_managers.append(self.pp_spec_manager)
self.message = 'Prepare frame: %s' % (frame_name)
elif ok == True and skip_frame == True:
self.message = 'Skip frame %s' % (frame_name)
elif ok == False:
print('s_plus: ' + str(s_plus) + ' old_s_plus: ' + str(old_s_plus))
print('old_signal_plus: ' + str(self.old_signal_plus))
print('signal_plus: ' + str(data_vector_segment.signal_plus))
raise Exception('Error for idx ' + str(self.idx))
if _pp_spec.inactive_start >= 0 and _pp_spec.inactive_stop >= 0:
#if time array is not None use it as array for cumulative time
if not self.time == None:
self.cum_inactive += pl.sum(
self.time[
_pp_spec.inactive_start:_pp_spec.inactive_stop])
else:
self.cum_inactive += pl.sum(
self.x_data[
_pp_spec.inactive_start:_pp_spec.inactive_stop])
self.old_signal_plus = data_vector_segment.signal_plus
self.idx = self.idx + 1
self._pp_spec_old = _pp_spec
def __generate_multiprocessing_movie__(movie_name, movie_dir,
movie_width, movie_height,
movie_fps, movie_frames,
movie_clean_frames):
"""
generating a movie with given specification using multiprocessing;
all frames are divided into excluded sets of files, for each set
a movie is create, in the next step all parts are joined to create
one final movie
"""
#delete previous partial listing files
command = 'rm %s' % as_path(movie_dir, '%s_lst_*' % (movie_name))
execute_command(command)
#create listing of all files
listing_file = str(as_path(movie_dir, movie_name + ".lst"))
#command = 'ls %s > %s' % (as_path(movie_dir, movie_frames), listing_file)
#a better version with no trouble with a limit of number of files of ls command
command = '(cd %s; find $PWD -name \'*.png\' | sort > %s)' % (movie_dir, listing_file)
execute_command(command)
#get number of movie frames
command = 'wc -l %s' % listing_file
count = int(execute_command(command, 1).split()[0])
#get bytes per line
command = 'head %s' % listing_file
bytes_per_line = int(len(execute_command(command, 1)))
#divide number of files frames per processors count
size = count / multiprocessing.cpu_count()
#split listing file into equal parts prefixed <movie_name>_lst_
command = '(cd %s; split -C %i %s %s_lst_)' % \
(movie_dir, bytes_per_line * size, listing_file, movie_name)
execute_command(command)
#delete all previous movie parts
command = 'rm %s' % as_path(movie_dir, '%s_part_*.avi' % (movie_name))
execute_command(command)
movie_specifications = []
#iterate over splits to create movie_specifications objects
command = 'ls ' + as_path(movie_dir, '%s_lst_*' % (movie_name))
for idx, frames_file in enumerate(run_command(command)):
frames_file = frames_file.replace('\n', '')
movie_specification = MovieSpecification(movie_name, movie_dir,
movie_width, movie_height, movie_fps, frames_file,
idx, movie_frames)
movie_specifications.append(movie_specification)
#run generation of partial movies
pool = multiprocessing.Pool(processes=multiprocessing.cpu_count())
#if not self.params.info_message_handler == None:
# self.params.info_message_handler('Generating frames'
# + (' ' * 20))
pool.map(__generate_movie__, movie_specifications)
pool.close()
#join all video part movies
movie_draft = movie_name + '_draft.avi'
command = '(cd %s; cat %s_part_*.avi > %s)' % (
movie_dir, movie_name, movie_draft)
execute_command(command)
#convert draft file into final movie file
output_file = '%s.avi' % (movie_name)
command = '(cd %s; mencoder %s -o %s -forceidx -ovc copy -oac copy)' \
% (movie_dir, movie_draft, output_file)
execute_command(command)
#delete draft movie
command = 'rm %s' % as_path(movie_dir, movie_draft)
execute_command(command)
#delete all movie parts
command = 'rm %s' % as_path(movie_dir, '%s_part_*.avi' % (movie_name))
execute_command(command)
#delete partial listing files
command = 'rm %s' % as_path(movie_dir, '%s_lst_*' % (movie_name))
execute_command(command)
# delete frames files
if movie_clean_frames:
command = 'cat %s | xargs rm ' % as_path(movie_dir, '%s.lst' % (movie_name))
execute_command(command)
#delete listing of all files
command = 'rm %s' % as_path(movie_dir, '%s.lst' % (movie_name))
execute_command(command)
return output_file