def display(self, ind=0, hist=False):
nb_images = 2
name_files = self.serie_arrays.get_name_files()[ind:ind + nb_images]
results_series = SerieOfArraysFromFiles(self.params.saving.path)
results = {
name: results_series.get_array_from_name(name)
for name in name_files[ind:ind + nb_images]
}
return super().display(ind, hist, results)
def __init__(self, params=None):
"""Set path for results and loads images as SerieOfArraysFromFiles."""
if params is None:
params = self.__class__.create_default_params()
self.params = params.preproc
path = params.preproc.series.path
if not os.path.exists(path):
path = params.preproc.series.path = os.path.expandvars(path)
self.serie_arrays = SerieOfArraysFromFiles(path)
self.tools = PreprocTools(params)
self.results = {}
class PreprocBase(object):
"""Preprocess series of images with various tools. """
@classmethod
def create_default_params(cls):
"""Class method returning the default parameters."""
params = ParamContainer(tag='params')
params._set_child('preproc')
params.preproc._set_child('series', attribs={'path': ''})
PreprocTools._complete_class_with_tools(params)
return params
def __init__(self, params=None):
"""Set path for results and loads images as SerieOfArraysFromFiles."""
if params is None:
params = self.__class__.create_default_params()
self.params = params.preproc
path = params.preproc.series.path
if not os.path.exists(path):
path = params.preproc.series.path = os.path.expandvars(path)
self.serie_arrays = SerieOfArraysFromFiles(path)
self.tools = PreprocTools(params)
self.results = {}
def __call__(self):
"""Apply all enabled preprocessing tools on the series of arrays
and saves them in self.results.
"""
name_files = self.serie_arrays.get_name_files()
for i, img in enumerate(self.serie_arrays.iter_arrays()):
name = name_files[i]
self.results[name] = self.tools(img)
def __init__(self, params=None):
"""Set path for results and loads images as SerieOfArraysFromFiles."""
if params is None:
params = self.__class__.create_default_params()
self.params = params.preproc
path = params.preproc.series.path
if not os.path.exists(path):
path = params.preproc.series.path = os.path.expandvars(path)
self.serie_arrays = SerieOfArraysFromFiles(path)
self.tools = PreprocTools(params)
self.results = {}
class PreprocBase(object):
"""Preprocess series of images with various tools. """
@classmethod
def create_default_params(cls):
"""Class method returning the default parameters."""
params = ParamContainer(tag='params')
params._set_child('preproc')
params.preproc._set_child('series', attribs={'path': ''})
PreprocTools._complete_class_with_tools(params)
return params
def __init__(self, params=None):
"""Set path for results and loads images as SerieOfArraysFromFiles."""
if params is None:
params = self.__class__.create_default_params()
self.params = params.preproc
path = params.preproc.series.path
if not os.path.exists(path):
path = params.preproc.series.path = os.path.expandvars(path)
self.serie_arrays = SerieOfArraysFromFiles(path)
self.tools = PreprocTools(params)
self.results = {}
def __call__(self):
"""Apply all enabled preprocessing tools on the series of arrays
and saves them in self.results.
"""
name_files = self.serie_arrays.get_name_files()
for i, img in enumerate(self.serie_arrays.iter_arrays()):
name = name_files[i]
self.results[name] = self.tools(img)
def __init__(self, args):
if str_error_import_textbox:
raise ImportError(str_error_import_textbox)
path_in = args.path
if os.path.isdir(path_in):
self.path_files = glob(os.path.join(path_in, "*"))
self.path_files = [
path for path in self.path_files if check_image(path)
]
self.path_files.sort()
ifile = 0
else:
path_file = glob(path_in)[0]
self.path_files = glob(os.path.join(os.path.split(path_file)[0], "*"))
self.path_files = [
path for path in self.path_files if check_image(path)
]
self.path_files.sort()
ifile = self.path_files.index(path_file)
if len(self.path_files) == 0:
raise ValueError("No image files detected.")
if len(self.path_files) == 1 and self.path_files[0].endswith(".cine"):
serie = SerieOfArraysFromFiles(self.path_files[0])
self.path_files = serie.get_path_arrays()
path_dir = os.path.split(self.path_files[0])[0]
self.nb_images = len(self.path_files)
print("Will use {} images in the dir {}".format(self.nb_images, path_dir))
self._buttons = {}
self._textboxes = {}
fig = self.fig = plt.figure()
fig.canvas.set_window_title(
path_dir + " (" + time_as_str()[-8:].replace("-", ":") + ")"
)
self.ax = fig.add_axes([0.07, 0.15, 0.7, 0.78])
self.maps = {}
try:
self.cmap = plt.cm.viridis
except AttributeError:
self.cmap = plt.cm.jet
self.ifile = ifile
self._last_was_increase = False
im = imread(self.path_files[ifile])
self.clim = [0, 0.99 * im.max()]
self._updating_clim = False
self.loadim(ifile, im)
name_file = self.get_namefile()
self.ax.set_title(name_file)
self._image_changing = False
function_buttons = [None] * len(name_buttons)
function_buttons[0] = self._decrease_ifile_n
function_buttons[1] = self._decrease_ifile
function_buttons[2] = self._increase_ifile
function_buttons[3] = self._increase_ifile_n
y = size_button / 3.0
for i, x in enumerate(x_buttons):
name = name_buttons[i]
func = function_buttons[i]
self._create_button(fig, [x, y, size_button, size_button], name, func)
self._n = 1
self._create_text(
fig,
[0.1, y, 2 * size_button, size_button],
"n = ",
self._submit_n,
"1",
)
self._create_text(
fig,
[0.87, 0.92, 1.5 * size_button, size_button],
"cmax = ",
self._change_cmax,
"{:.2f}".format(self.clim[1]),
)
self._create_text(
fig,
[0.87, 0.1, 1.5 * size_button, size_button],
"cmin = ",
self._change_cmin,
"{:.2f}".format(self.clim[0]),
)
self._create_button(
fig, [0.65, 0.945, 1.2 * size_button, 0.045], "reload", self.reloadim
)
self._create_button(
fig, [0.85, y, size_button, size_button], "auto", self.set_autoclim
)
cax = fig.add_axes([0.83, 0.2, 0.07, 0.7])
self.cbar = fig.colorbar(self.mappable, cax=cax)
fig.canvas.mpl_connect("key_press_event", self.onclick)
print("press alt+h for help")
plt.show()