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Commit 217e78a7 authored by amichaut's avatar amichaut
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quiet flag replaced quiet count

parent fba7cfd7
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track_analyzer/plotting.py
View file @ 217e78a7
......@@ -110,7 +110,7 @@ def plot_cmap(plot_dir, label, cmap, vmin, vmax, plot_config=None, suffix=''):
def plot_traj(df, frame, data_dir, groups=None, image={'image_fn': None, 't_dim': None, 'z_dim': None}, plot_dir=None,
show_plot=False, dim=3, plot_config=None,traj_parameters=None,quiet=False):
show_plot=False, dim=3, plot_config=None,traj_parameters=None,quiet=0):
"""
Plot all trajectories of a given frame on an image if traj_parameters['no_bkg'] is False and an image is given.
Plots can be color coded z value, by groups, or with random colors (traj_parameters['color_code']='z' or 'group' or 'random' or 'none')
......@@ -118,7 +118,7 @@ def plot_traj(df, frame, data_dir, groups=None, image={'image_fn': None, 't_dim'
It can be plotted in 3D with plot3D, elevation and angle set the 3D view
"""
if not quiet:
if quiet < 1:
sys.stdout.write("\033[K") # go back to previous line
print('plotting frame {}'.format(int(frame)), flush=True, end='\r')
......@@ -284,10 +284,10 @@ def plot_traj(df, frame, data_dir, groups=None, image={'image_fn': None, 't_dim'
def plot_scalar_field(data_dir, df, data, field, frame, image={'image_fn': None, 't_dim': None, 'z_dim': None},
map_param={'no_bkg': False, 'vlim': None, 'show_axis': False, 'cmap': 'plasma'},
plot_dir=None, plot_config=None, quiet=False, dont_save=False):
plot_dir=None, plot_config=None, quiet=0, dont_save=False):
"""Plot scalar field as colormap. The data needs to be generated before. """
if not quiet:
if quiet < 1:
sys.stdout.write("\033[K") # go back to previous line
print('plotting {} {}'.format(field, int(frame)), flush=True, end='\r')
......@@ -364,10 +364,10 @@ def plot_vector_field(data_dir, df, data, field, frame, plot_on_field=None, dim=
image={'image_fn': None, 't_dim': None, 'z_dim': None},
map_param={'no_bkg': False, 'vlim': None, 'show_axis': False, 'cmap': 'plasma',
'size_factor': 1},
plot_dir=None, plot_config=None, quiet=False):
plot_dir=None, plot_config=None, quiet=0):
""" Plot vector field"""
if not quiet:
if quiet < 1:
sys.stdout.write("\033[K") # go back to previous line
print('plotting {} {}'.format(field, int(frame)), flush=True, end='\r')
......@@ -455,7 +455,7 @@ def plot_vector_field(data_dir, df, data, field, frame, plot_on_field=None, dim=
def plot_Voronoi(data_dir, df, frame, data, show_local_area=True,
image={'image_fn': None, 't_dim': None, 'z_dim': None},
map_param={'no_bkg': False, 'vlim': None, 'show_axis': False,'cmap':'plasma','size_factor': 1,'line_width':1.},
plot_dir=None, plot_config=None, dont_print_count=False,quiet=False):
plot_dir=None, plot_config=None, dont_print_count=False,quiet=0):
"""
Plot Voronoi tesselation and local area in 2D only.
:param data_dir:
......@@ -471,7 +471,7 @@ def plot_Voronoi(data_dir, df, frame, data, show_local_area=True,
:return:
"""
if not quiet:
if quiet < 1:
sys.stdout.write("\033[K") # go back to previous line
print('plotting {} {}'.format('voronoi', int(frame)), flush=True, end='\r')
......@@ -920,7 +920,7 @@ def view_traj(df, image=None, z_step=1):
def plot_all_traj(data_dir, df, image={'image_fn': None, 't_dim': None, 'z_dim': None}, parallelize=False, dim=3,
plot_dir=None,traj_parameters=None,plot_config=None,quiet=False):
plot_dir=None,traj_parameters=None,plot_config=None,quiet=0):
"""Plot traj for all frames"""
# plotting directory
......@@ -1021,7 +1021,7 @@ def plot_all_traj(data_dir, df, image={'image_fn': None, 't_dim': None, 'z_dim':
def plot_all_scalar_fields(data_dir, df, data, field, image={'image_fn': None, 't_dim': None, 'z_dim': None},
map_param={'no_bkg': False, 'vlim': None, 'show_axis': False, 'cmap': 'plasma'},
plot_dir=None, plot_config=None, quiet=False):
plot_dir=None, plot_config=None, quiet=0):
"""Plot scalar fields as colormap for all frames."""
# plotting directory
......@@ -1073,7 +1073,7 @@ def plot_all_vector_fields(data_dir, df, data, field, plot_on_field=None, dim=3,
image={'image_fn': None, 't_dim': None, 'z_dim': None},
map_param={'no_bkg': False, 'vlim': None, 'show_axis': False, 'cmap': 'plasma',
'size_factor': 1},
plot_dir=None, plot_config=None, quiet=False):
plot_dir=None, plot_config=None, quiet=0):
"""Plot vector fields for all frames."""
# plotting directory
......@@ -1122,7 +1122,7 @@ def plot_all_vector_fields(data_dir, df, data, field, plot_on_field=None, dim=3,
def plot_all_Voronoi(data_dir, df, data, show_local_area=True, df_mean = None,
image={'image_fn': None, 't_dim': None, 'z_dim': None},
map_param=None,plot_dir=None, plot_config=None,quiet=False):
map_param=None,plot_dir=None, plot_config=None,quiet=0):
"""
Plot Voronoi for all frames and calculate voronoi cell area.
"""
......
track_analyzer/scripts/analyze_maps.py
View file @ 217e78a7
......@@ -35,7 +35,7 @@ from track_analyzer import calculate as tca
def map_analysis(data_dir, data=None, image=None, refresh=False, parallelize=False, filters=None,
plot_config=None, map_config=None, data_config=None, quiet=False):
plot_config=None, map_config=None, data_config=None, quiet=0):
"""Container method to plot a series of maps given by field_values. Manual vlim to colormap can be passed."""
map_dir = osp.join(data_dir, 'map_analysis')
......@@ -140,7 +140,8 @@ def map_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fal
dir_name = '_' + subset_name if subset_name != '' else ''
dir_name_ = '{}{}'.format(len(tpr.listdir_nohidden(map_dir)) + 1, dir_name)
print(r"Analyzing subset {} ".format(i + 1, dir_name_))
if quiet < 2:
print(r"Analyzing subset {} ".format(i + 1, dir_name_))
sub_dir = osp.join(map_dir, dir_name_)
sub_dir = sub_dir + '_1' if osp.exists(sub_dir) else sub_dir # dont overwrite existing dir
tpr.safe_mkdir(sub_dir)
......@@ -202,7 +203,7 @@ def map_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fal
# plot data
scalar_fields_ = {**scalar_fields, **vector_mean} # merge scalar data in one single dict
for field in scalar_fields_.keys():
if not quiet:
if quiet < 2:
print("Plotting scalar fields...")
if plot_config['save_as_stack']:
plot_dir = sub_dir
......@@ -215,7 +216,7 @@ def map_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fal
tpl.plot_all_scalar_fields(data_dir, df, field_data, field, image=image, map_param=map_param_,
plot_dir=plot_dir, plot_config=plot_config, quiet=quiet)
for field in vector_fields.keys():
if not quiet:
if quiet < 2:
print("Plotting vector fields...")
if plot_config['save_as_stack']:
plot_dir = sub_dir
......@@ -258,9 +259,10 @@ def parse_args(args=None):
help=argparse.SUPPRESS)
parser.add_argument('-q', '--quiet',
action="store_true",
action="count",
default=False,
help='do not display main log output')
help="""decrease verbosity level. There are 3 levels:
display detailed log (default), display simple log (-q), display only warning and errors (-qq)""")
parsed_args = parser.parse_args(args)
......
track_analyzer/scripts/analyze_tracks.py
View file @ 217e78a7
......@@ -35,7 +35,7 @@ from track_analyzer import calculate as tca
def traj_analysis(data_dir, data=None, image=None, refresh=False, parallelize=False, filters=None, plot_config=None,
traj_config=None, data_config=None, quiet=False):
traj_config=None, data_config=None, quiet=0):
"""Container method to run analysis related to cell trajectories."""
traj_dir = osp.join(data_dir, 'traj_analysis')
......@@ -126,7 +126,8 @@ def traj_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fa
dir_name = '_' + subset_name if subset_name != '' else ''
dir_name_ = '{}{}'.format(len(tpr.listdir_nohidden(traj_dir)) + 1, dir_name)
print(r"Analyzing subset #{}, named: {}".format(i + 1, dir_name_))
if quiet < 2:
print(r"Analyzing subset #{}, named: {}".format(i + 1, dir_name_))
sub_dir = osp.join(traj_dir, dir_name_)
sub_dir = sub_dir + '_1' if osp.exists(sub_dir) else sub_dir # dont overwrite existing dir
tpr.safe_mkdir(sub_dir)
......@@ -158,20 +159,20 @@ def traj_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fa
# plot trajectories
if traj_config_['run']:
if not quiet:
if quiet < 2:
print("Plotting trajectories...")
tpl.plot_all_traj(data_dir, df, image=image, traj_parameters=traj_config_, parallelize=parallelize,
dim=dim, plot_dir=sub_dir, plot_config=plot_config, quiet=quiet)
if total_traj_config['run']:
if not quiet:
if quiet < 2:
print("Plotting total trajectories")
tpl.plot_total_traj(data_dir, df, dim=dim, plot_dir=sub_dir, plot_config=plot_config,
specific_config=total_traj_config)
# MSD analysis
if MSD_config['run']:
if not quiet:
if quiet < 2:
print("MSD analysis...")
df_prop = tpl.plot_all_MSD(data_dir, df, df_out=df_prop, fit_model=MSD_config['MSD_model'],
MSD_parameters=MSD_config, plot_config=plot_config, plot_dir=sub_dir, hue=hue,
......@@ -180,7 +181,7 @@ def traj_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fa
# Voronoi analysis
if voronoi_config['run']:
if not quiet:
if quiet < 2:
print("Voronoi analysis...")
vor_data = tca.compute_all_Voronoi(data_dir, df, outdir=sub_dir,compute_local_area=voronoi_config['compute_local_area'],
area_threshold=voronoi_config['area_threshold'],df_mean=df_prop)
......@@ -205,7 +206,7 @@ def traj_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fa
if 'var_list' in hist_config.keys():
if len(hist_config['var_list']) > 0:
if not quiet:
if quiet < 2:
print("Plotting parameters histograms...")
for p in hist_config['var_list']:
tpl.plot_param_hist(data_dir, p, df, plot_config=plot_config, plot_dir=sub_dir, hue=hue,
......@@ -213,7 +214,7 @@ def traj_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fa
if 'mean_var_list' in hist_config.keys():
if len(hist_config['mean_var_list']) > 0:
if not quiet:
if quiet < 2:
print("Plotting whole-track histograms...")
for p in hist_config['mean_var_list']:
tpl.plot_param_hist(data_dir, p, df_prop, plot_config=plot_config, plot_dir=sub_dir, prefix='track_',
......@@ -225,7 +226,7 @@ def traj_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fa
if 'couple_list' in scatter_config.keys():
if len(scatter_config['couple_list']) > 0:
if not quiet:
if quiet < 2:
print("Plotting couples of parameters...")
for param_vs_param in scatter_config['couple_list']:
x_param, y_param = param_vs_param
......@@ -234,7 +235,7 @@ def traj_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fa
if 'mean_couple_list' in scatter_config.keys():
if len(scatter_config['mean_couple_list']) > 0:
if not quiet:
if quiet < 2:
print("Plotting couples of whole-track parameters...")
for param_vs_param in scatter_config['mean_couple_list']:
x_param, y_param = param_vs_param
......@@ -271,9 +272,10 @@ def parse_args(args=None):
help=argparse.SUPPRESS)
parser.add_argument('-q', '--quiet',
action="store_true",
action="count",
default=False,
help='do not display main log output')
help="""decrease verbosity level. There are 3 levels:
display detailed log (default), display simple log (-q), display only warning and errors (-qq)""")
parsed_args = parser.parse_args(args)
......
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