Skip to content

GitLab

Commit fba7cfd7 authored by amichaut's avatar amichaut
Browse files

updated copyright + replaced verbosity by quiet flag

parent 7ca8f1ac
Expand all Hide whitespace changes
Inline Side-by-side
doc/source/_static/example/load_tracking.py
View file @ fba7cfd7
......@@ -3,7 +3,7 @@
# Authors: Arthur Michaut #
# Copyright 2016-2019 Harvard Medical School and Brigham and #
# Women's Hospital #
# Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738 #
# Copyright 2019-2022 Institut Pasteur and CNRS–UMR3738 #
# See the COPYRIGHT file for details #
# #
# This file is part of Track Analyzer package. #
......
doc/source/developer_guide/index.rst
View file @ fba7cfd7
......@@ -2,7 +2,7 @@
Authors: Arthur Michaut
Copyright 2016-2019 Harvard Medical School and Brigham and
Women's Hospital
Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738
Copyright 2019-2022 Institut Pasteur and CNRS–UMR3738
See the COPYRIGHT file for details
This file is part of Track Analyzer package.
......
doc/source/user_guide/index.rst
View file @ fba7cfd7
......@@ -2,7 +2,7 @@
Authors: Arthur Michaut
Copyright 2016-2019 Harvard Medical School and Brigham and
Women's Hospital
Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738
Copyright 2019-2022 Institut Pasteur and CNRS–UMR3738
See the COPYRIGHT file for details
This file is part of Track Analyzer package.
......
doc/source/user_guide/installation.rst
View file @ fba7cfd7
......@@ -2,7 +2,7 @@
Authors: Arthur Michaut
Copyright 2016-2019 Harvard Medical School and Brigham and
Women's Hospital
Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738
Copyright 2019-2022 Institut Pasteur and CNRS–UMR3738
See the COPYRIGHT file for details
This file is part of Track Analyzer package.
......
doc/source/user_guide/quickstart.rst
View file @ fba7cfd7
......@@ -2,7 +2,7 @@
Authors: Arthur Michaut
Copyright 2016-2019 Harvard Medical School and Brigham and
Women's Hospital
Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738
Copyright 2019-2022 Institut Pasteur and CNRS–UMR3738
See the COPYRIGHT file for details
This file is part of Track Analyzer package.
......
run_TA.ipynb
View file @ fba7cfd7
This diff is collapsed.
This diff is collapsed.
setup.py
View file @ fba7cfd7
......@@ -3,7 +3,7 @@
# Authors: Arthur Michaut #
# Copyright 2016-2019 Harvard Medical School and Brigham and #
# Women's Hospital #
# Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738 #
# Copyright 2019-2022 Institut Pasteur and CNRS–UMR3738 #
# See the COPYRIGHT file for details #
# #
# This file is part of Track Analyzer package. #
......
track_analyzer/__init__.py
View file @ fba7cfd7
......@@ -3,7 +3,7 @@
# Authors: Arthur Michaut #
# Copyright 2016-2019 Harvard Medical School and Brigham and #
# Women's Hospital #
# Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738 #
# Copyright 2019-2022 Institut Pasteur and CNRS–UMR3738 #
# See the COPYRIGHT file for details #
# #
# This file is part of Track Analyzer package. #
......
track_analyzer/calculate.py
View file @ fba7cfd7
......@@ -3,7 +3,7 @@
# Authors: Arthur Michaut #
# Copyright 2016-2019 Harvard Medical School and Brigham and #
# Women's Hospital #
# Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738 #
# Copyright 2019-2022 Institut Pasteur and CNRS–UMR3738 #
# See the COPYRIGHT file for details #
# #
# This file is part of Track Analyzer package. #
......
track_analyzer/deprecated.py
View file @ fba7cfd7
......@@ -3,7 +3,7 @@
# Authors: Arthur Michaut #
# Copyright 2016-2019 Harvard Medical School and Brigham and #
# Women's Hospital #
# Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738 #
# Copyright 2019-2022 Institut Pasteur and CNRS–UMR3738 #
# See the COPYRIGHT file for details #
# #
# This file is part of Track Analyzer package. #
......
track_analyzer/plotting.py
View file @ fba7cfd7
......@@ -3,7 +3,7 @@
# Authors: Arthur Michaut #
# Copyright 2016-2019 Harvard Medical School and Brigham and #
# Women's Hospital #
# Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738 #
# Copyright 2019-202é Institut Pasteur and CNRS–UMR3738 #
# See the COPYRIGHT file for details #
# #
# This file is part of Track Analyzer package. #
......@@ -110,15 +110,17 @@ 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):
show_plot=False, dim=3, plot_config=None,traj_parameters=None,quiet=False):
"""
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')
The trajectory path can be removed to keep only the dots if traj_parameters['traj'] is False.
It can be plotted in 3D with plot3D, elevation and angle set the 3D view
"""
sys.stdout.write("\033[K") # go back to previous line
print('plotting frame {}'.format(int(frame)), flush=True, end='\r')
if not quiet:
sys.stdout.write("\033[K") # go back to previous line
print('plotting frame {}'.format(int(frame)), flush=True, end='\r')
# get config parameters
plot_config = make_plot_config() if plot_config is None else plot_config
......@@ -282,10 +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, dont_print_count=False, dont_save=False):
plot_dir=None, plot_config=None, quiet=False, dont_save=False):
"""Plot scalar field as colormap. The data needs to be generated before. """
if not dont_print_count:
if not quiet:
sys.stdout.write("\033[K") # go back to previous line
print('plotting {} {}'.format(field, int(frame)), flush=True, end='\r')
......@@ -362,10 +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, dont_print_count=False):
plot_dir=None, plot_config=None, quiet=False):
""" Plot vector field"""
if not dont_print_count:
if not quiet:
sys.stdout.write("\033[K") # go back to previous line
print('plotting {} {}'.format(field, int(frame)), flush=True, end='\r')
......@@ -453,7 +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):
plot_dir=None, plot_config=None, dont_print_count=False,quiet=False):
"""
Plot Voronoi tesselation and local area in 2D only.
:param data_dir:
......@@ -469,7 +471,7 @@ def plot_Voronoi(data_dir, df, frame, data, show_local_area=True,
:return:
"""
if not dont_print_count:
if not quiet:
sys.stdout.write("\033[K") # go back to previous line
print('plotting {} {}'.format('voronoi', int(frame)), flush=True, end='\r')
......@@ -694,6 +696,8 @@ def plot_param_vs_param(data_dir, x_param, y_param, df=None, hue=None, hue_order
if plot_config['despine']:
sns.despine(fig)
ax.legend(frameon=False)
filename = osp.join(plot_dir, prefix + '{}_vs_{}{}{}'.format(y_param, x_param, suffix, plot_config['format']))
fig.savefig(filename, dpi=plot_config['dpi'], bbox_inches='tight')
plt.close(fig)
......@@ -737,16 +741,13 @@ def plot_param_hist(data_dir, param, df=None, hue=None, hue_order=None, hist=Tru
df = df[np.isfinite(df[param])]
kind = "hist" if hist else "kde"
g = sns.displot(data=df, x=param, hue=hue, kind=kind, kde=kde,facet_kws={'legend_out':False})
sns.move_legend(g, "upper right", frameon=False)
g = sns.displot(data=df, x=param, hue=hue, kind=kind, kde=kde,facet_kws={'legend_out':False,'despine':plot_config['despine']})
sns.move_legend(g, "upper right", frameon=False, bbox_to_anchor=[0.95, 0.95],title=None)
fig = g.figure
ax = g.ax
fig.set_size_inches(figsize[0], figsize[1])
ax.set_xlabel(param_label)
if plot_config['despine']:
sns.despine(fig)
filename = osp.join(plot_dir, prefix + '{}_hist{}{}'.format(param, suffix, plot_config['format']))
fig.savefig(filename, dpi=plot_config['dpi'], bbox_inches='tight')
plt.close(fig)
......@@ -919,7 +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):
plot_dir=None,traj_parameters=None,plot_config=None,quiet=False):
"""Plot traj for all frames"""
# plotting directory
......@@ -1003,7 +1004,7 @@ def plot_all_traj(data_dir, df, image={'image_fn': None, 't_dim': None, 'z_dim':
frame = int(frame)
fig = plot_traj(df, frame, data_dir, groups=groups, image=image, plot_dir=plot_dir,
traj_parameters=traj_parameters,
dim=dim, plot_config=plot_config)
dim=dim, plot_config=plot_config,quiet=quiet)
# append to stack
if save_as_stack:
......@@ -1020,7 +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, dont_print_count=False):
plot_dir=None, plot_config=None, quiet=False):
"""Plot scalar fields as colormap for all frames."""
# plotting directory
......@@ -1051,7 +1052,8 @@ def plot_all_scalar_fields(data_dir, df, data, field, image={'image_fn': None, '
for frame in np.sort(df['frame'].unique()):
frame = int(frame)
fig = plot_scalar_field(data_dir, df, data, field, frame, image=image,
map_param=map_param_, plot_dir=plot_dir, plot_config=plot_config)
map_param=map_param_, plot_dir=plot_dir,
plot_config=plot_config, quiet=quiet)
# append to stack
if save_as_stack:
......@@ -1071,7 +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, dont_print_count=False):
plot_dir=None, plot_config=None, quiet=False):
"""Plot vector fields for all frames."""
# plotting directory
......@@ -1104,7 +1106,7 @@ def plot_all_vector_fields(data_dir, df, data, field, plot_on_field=None, dim=3,
for frame in np.sort(df['frame'].unique()):
frame = int(frame)
fig = plot_vector_field(data_dir, df, data, field, frame, plot_on_field=plot_on_field, dim=dim, image=image,
map_param=map_param, plot_dir=plot_dir, plot_config=plot_config)
map_param=map_param, plot_dir=plot_dir, plot_config=plot_config, quiet=quiet)
# append to stack
if save_as_stack:
......@@ -1120,7 +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, dont_print_count=False):
map_param=None,plot_dir=None, plot_config=None,quiet=False):
"""
Plot Voronoi for all frames and calculate voronoi cell area.
"""
......@@ -1176,7 +1178,7 @@ def plot_all_Voronoi(data_dir, df, data, show_local_area=True, df_mean = None,
for frame in np.sort(df['frame'].unique()):
frame = int(frame)
fig = plot_Voronoi(data_dir, df, frame, data, show_local_area=show_local_area, image=image, map_param=map_param,
plot_dir=plot_dir, plot_config=plot_config, dont_print_count=dont_print_count)
plot_dir=plot_dir, plot_config=plot_config, quiet=quiet)
# append to stack
if save_as_stack:
......
track_analyzer/prepare.py
View file @ fba7cfd7
......@@ -3,7 +3,7 @@
# Authors: Arthur Michaut #
# Copyright 2016-2019 Harvard Medical School and Brigham and #
# Women's Hospital #
# Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738 #
# Copyright 2019-2022 Institut Pasteur and CNRS–UMR3738 #
# See the COPYRIGHT file for details #
# #
# This file is part of Track Analyzer package. #
......@@ -1201,11 +1201,9 @@ def load_config(data_dir, verbose=False):
if f.endswith('.csv'):
out_dict[f[:-4]] = load_dict(osp.join(config_dir, f))
else:
if verbose:
print("WARNING: config is not a directory. Config not loaded.")
print("WARNING: config is not a directory. Config not loaded.")
else:
if verbose:
print("WARNING: no config directory. Config not loaded.")
print("WARNING: no config directory. Config not loaded.")
return out_dict
......
track_analyzer/scripts/__init__.py
View file @ fba7cfd7
......@@ -3,7 +3,7 @@
# Authors: Arthur Michaut #
# Copyright 2016-2019 Harvard Medical School and Brigham and #
# Women's Hospital #
# Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738 #
# Copyright 2019-2022 Institut Pasteur and CNRS–UMR3738 #
# See the COPYRIGHT file for details #
# #
# This file is part of Track Analyzer package. #
......
track_analyzer/scripts/analyze_maps.py
View file @ fba7cfd7
......@@ -3,7 +3,7 @@
# Authors: Arthur Michaut #
# Copyright 2016-2019 Harvard Medical School and Brigham and #
# Women's Hospital #
# Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738 #
# Copyright 2019-2022 Institut Pasteur and CNRS–UMR3738 #
# See the COPYRIGHT file for details #
# #
# This file is part of Track Analyzer package. #
......@@ -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):
plot_config=None, map_config=None, data_config=None, quiet=False):
"""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')
......@@ -202,6 +202,8 @@ 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:
print("Plotting scalar fields...")
if plot_config['save_as_stack']:
plot_dir = sub_dir
else: # save series of images in a separate directory
......@@ -211,8 +213,10 @@ def map_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fal
map_param_['vlim'] = scalar_fields_[field]['vlim'] if 'vlim' in scalar_fields_[field].keys() else None
map_param_['cmap'] = scalar_fields_[field]['cmap'] if 'cmap' in scalar_fields_[field].keys() else 'plasma'
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, dont_print_count=False)
plot_dir=plot_dir, plot_config=plot_config, quiet=quiet)
for field in vector_fields.keys():
if not quiet:
print("Plotting vector fields...")
if plot_config['save_as_stack']:
plot_dir = sub_dir
else: # save series of images in a separate directory
......@@ -222,7 +226,7 @@ def map_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fal
map_param_['vlim'] = vector_fields[field]['vlim']
tpl.plot_all_vector_fields(data_dir, df, field_data, field, image=image, plot_on_field=vector_fields[field],
dim=3, map_param=map_param_, plot_dir=plot_dir, plot_config=plot_config,
dont_print_count=False)
quiet=quiet)
return df_list
......@@ -253,9 +257,10 @@ def parse_args(args=None):
default=False,
help=argparse.SUPPRESS)
parser.add_argument('-v', '--verbose',
action="store_true",
help='Increase verbosity of output')
parser.add_argument('-q', '--quiet',
action="store_true",
default=False,
help='do not display main log output')
parsed_args = parser.parse_args(args)
......@@ -271,6 +276,7 @@ def main(args=None):
data_dir = osp.realpath(parsed_args.data_dir)
refresh = parsed_args.refresh
parallelize = parsed_args.parallelize
quiet = parsed_args.quiet
if not osp.exists(data_dir):
raise Exception("ERROR: the passed data directory does not exist. Aborting...")
......@@ -279,7 +285,7 @@ def main(args=None):
raise Exception("ERROR: the passed data directory is not a directory. Aborting...")
# Load config
config = tpr.load_config(data_dir, verbose=parsed_args.verbose)
config = tpr.load_config(data_dir)
# Check config
mandatory_config = ["filters", "plot_config", "data_config"]
......@@ -297,6 +303,7 @@ def main(args=None):
map_analysis(data_dir,
refresh=refresh,
parallelize=parallelize,
quiet=quiet,
filters=config["filters"],
plot_config=config["plot_config"],
map_config=map_config,
......
track_analyzer/scripts/analyze_tracks.py
View file @ fba7cfd7
......@@ -3,7 +3,7 @@
# Authors: Arthur Michaut #
# Copyright 2016-2019 Harvard Medical School and Brigham and #
# Women's Hospital #
# Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738 #
# Copyright 2019-2022 Institut Pasteur and CNRS–UMR3738 #
# See the COPYRIGHT file for details #
# #
# This file is part of Track Analyzer package. #
......@@ -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):
traj_config=None, data_config=None, quiet=False):
"""Container method to run analysis related to cell trajectories."""
traj_dir = osp.join(data_dir, 'traj_analysis')
......@@ -158,18 +158,21 @@ def traj_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fa
# plot trajectories
if traj_config_['run']:
print("Plotting trajectories...")
if not quiet:
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)
dim=dim, plot_dir=sub_dir, plot_config=plot_config, quiet=quiet)
if total_traj_config['run']:
print("Plotting total trajectories")
if not quiet:
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']:
print("MSD analysis...")
if not quiet:
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,
hue_order=hue_order)
......@@ -177,6 +180,8 @@ def traj_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fa
# Voronoi analysis
if voronoi_config['run']:
if not quiet:
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)
# update csv files with area data
......@@ -184,13 +189,15 @@ def traj_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fa
df.to_csv(csv_fn)
if voronoi_config['plot']:
if len(df_list) > 1 and subset_analysis == 'together':
print("WARNING: there is no color code to identify subsets in Voronoi diagram plots")
if plot_config['save_as_stack']:
plot_dir = sub_dir
else: # save series of images in a separate directory
plot_dir = osp.join(sub_dir, 'voronoi')
tpr.safe_mkdir(plot_dir)
tpl.plot_all_Voronoi(data_dir, df, vor_data, show_local_area=voronoi_config['show_local_area'], image=image,
map_param=voronoi_config, plot_dir=plot_dir, plot_config=plot_config, dont_print_count=False)
map_param=voronoi_config, plot_dir=plot_dir, plot_config=plot_config, quiet=quiet)
if hist_config['run']:
fn = osp.join(config_dir, 'hist_config.csv')
......@@ -198,14 +205,16 @@ 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:
print("Plotting parameters histograms...")
if not quiet:
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,
hue_order=hue_order)
if 'mean_var_list' in hist_config.keys():
if len(hist_config['mean_var_list']) > 0:
print("Plotting whole-track histograms...")
if not quiet:
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_',
hue=hue, hue_order=hue_order)
......@@ -216,7 +225,8 @@ 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:
print("Plotting couples of parameters...")
if not quiet:
print("Plotting couples of parameters...")
for param_vs_param in scatter_config['couple_list']:
x_param, y_param = param_vs_param
tpl.plot_param_vs_param(data_dir, x_param, y_param, df, plot_dir=sub_dir, plot_config=plot_config,
......@@ -224,7 +234,8 @@ 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:
print("Plotting couples of whole-track parameters...")
if not quiet:
print("Plotting couples of whole-track parameters...")
for param_vs_param in scatter_config['mean_couple_list']:
x_param, y_param = param_vs_param
tpl.plot_param_vs_param(data_dir, x_param, y_param, df_prop, plot_dir=sub_dir, plot_config=plot_config,
......@@ -259,9 +270,10 @@ def parse_args(args=None):
default=False,
help=argparse.SUPPRESS)
parser.add_argument('-v', '--verbose',
action="store_true",
help='Increase verbosity of output')
parser.add_argument('-q', '--quiet',
action="store_true",
default=False,
help='do not display main log output')
parsed_args = parser.parse_args(args)
......@@ -277,6 +289,7 @@ def main(args=None):
data_dir = osp.realpath(parsed_args.data_dir)
refresh = parsed_args.refresh
parallelize = parsed_args.parallelize
quiet = parsed_args.quiet
if not osp.exists(data_dir):
raise Exception("ERROR: the passed data directory does not exist. Aborting...")
......@@ -285,7 +298,7 @@ def main(args=None):
raise Exception("ERROR: the passed data directory is not a directory. Aborting...")
# Load config
config = tpr.load_config(data_dir, verbose=parsed_args.verbose)
config = tpr.load_config(data_dir)
# Check config
mandatory_config = ["filters", "plot_config", "data_config"]
......@@ -303,6 +316,7 @@ def main(args=None):
traj_analysis(data_dir,
refresh=refresh,
parallelize=parallelize,
quiet=quiet,
filters=config["filters"],
plot_config=config["plot_config"],
traj_config=traj_config,
......
track_analyzer/scripts/compare_datasets.py
View file @ fba7cfd7
......@@ -3,7 +3,7 @@
# Authors: Arthur Michaut #
# Copyright 2016-2019 Harvard Medical School and Brigham and #
# Women's Hospital #
# Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738 #
# Copyright 2019-2022 Institut Pasteur and CNRS–UMR3738 #
# See the COPYRIGHT file for details #
# #
# This file is part of Track Analyzer package. #
......
track_analyzer/synthetic_data.py
View file @ fba7cfd7
......@@ -3,7 +3,7 @@
# Authors: Arthur Michaut #
# Copyright 2016-2019 Harvard Medical School and Brigham and #
# Women's Hospital #
# Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738 #
# Copyright 2019-2022 Institut Pasteur and CNRS–UMR3738 #
# See the COPYRIGHT file for details #
# #
# This file is part of Track Analyzer package. #
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment