PartSeg.common_backend package

Module contents

This module contains non gui Qt based components

PartSeg.common_backend.napari_get_settings(path=None)

Return type:

NapariSettings

Submodules

PartSeg.common_backend.abstract_class module

class PartSeg.common_backend.abstract_class.QtMeta(name, bases, namespace, /, **kwargs)

Bases: wrappertype, ABCMeta

Class to solve metaclass conflict for multiple inheritance:

TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclass of all its bases

>>> class A:
...    pass
...
>>> class Test(QObject, A, metaclass=QtMeta):
...    pass

PartSeg.common_backend.base_argparser module

class PartSeg.common_backend.base_argparser.CustomParser(*args, **kwargs)

Bases: ArgumentParser

Argument parser with set of predefined flags:

1. --no_report - disable error reporting, still showing dialog with information. Set state_store.report_errors.

2. --no_dialog - disable error reporting and showing dialog. Exceptions will be printed on stderr. Set state_store.show_error_dialog.

3. --no_update - disable check for updates on application startup

   Set state_store.check_for_updates.

4. --save_suffix - add special suffix to directory contains saved state. designed to allow separate projects.

   Set state_store.save_suffix.

5. --save_directory - set custom save directory. default can be previewed in Help > State directory

   from PartSeg main menu, Set state_store.save_folder.

6. --inner_plugins - designed to hide part plugin from default start.

   Set state_store.custom_plugin_load.

7. --develop – for developer purpose. Allow to reload part of Program without restarting. May be unstable.

   Set state_store.develop. Base on this PartSeg.common_gui.advanced_tabs.AdvancedWindow constructor add developer tab.

parse_args(args=None, namespace=None)

overload of argparse.ArgumentParser.parse_args(). Set flags like described in class documentation.

PartSeg.common_backend.base_argparser.proper_path(val)

Check if val is proper path in current system

Raises:

argparse.ArgumentTypeError – on validation error

PartSeg.common_backend.base_argparser.proper_suffix(val)

check if val contains only alphanumeric characters

Raises:

argparse.ArgumentTypeError – on validation error

PartSeg.common_backend.base_settings module

class PartSeg.common_backend.base_settings.BaseSettings(json_path, profile_name='default')

Bases: ViewSettings

Variables:

• json_folder_path – default location for saving/loading settings data

• last_executed_algorithm – name of last executed algorithm.

• save_locations_keys – list of names of distinct save location. location are stored in “io”

add_history_element(elem)

Return type:

None

add_last_files(file_path, load_method)

add_last_files_multiple(file_paths, load_method)

add_load_files_history(file_path, load_method)

add_path_history(dir_path)

Save path in history of visited directories. Store only 10 last

algorithm_changed

Signal emitted when current algorithm should be changed

static cmp_history_element(el1, el2)

connect_(key_path, callback)

dump(folder_path=None)

Save current application settings to disc.

Parameters:

folder_path (Union[Path, str, None]) – path to directory in which data should be saved. If is None then use json_folder_path

dump_part(file_path, path_in_dict, names=None)

get(key_path, default=None)

Function for getting general state (not visualization). This is accessor to get() of inner variable.

Parameters:

• key_path (str) – dot separated path

• default – default value if key is missed

get_algorithm(key_path, default=None)

Function for getting last algorithm used information. This is accessor to get() of inner variable.

Parameters:

• key_path (str) – dot separated path

• default – default value if key is missed

get_history()

Return type:

list[HistoryElement]

get_last_files()

Return type:

list[tuple[tuple[Union[str, Path], ...], str]]

get_last_files_multiple()

Return type:

list[tuple[tuple[Union[str, Path], ...], str]]

get_path_history()

return list containing last 10 elements added with add_path_history() and last opened in each category form save_location_keys

Return type:

list[str]

get_project_info()

Get all information needed to save project

Return type:

ProjectInfoBase

get_save_list()

List of files in which program save the state.

Return type:

list[SaveSettingsDescription]

history_current_element()

Return type:

HistoryElement

history_next_element()

Return type:

HistoryElement

history_pop()

Return type:

Optional[HistoryElement]

history_redo_clean()

Return type:

None

history_redo_size()

Return type:

int

history_size()

Return type:

int

json_encoder_class

alias of PartSegEncoder

load(folder_path=None)

Load settings state from given directory

Parameters:

folder_path (Union[Path, str, None]) – path to directory in which data should be saved. If is None then use json_folder_path

static load_metadata()

property mask

mask_changed

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

property points

points_changed

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

request_load_files(list)

Signal mask changed signal

save_locations_keys: ClassVar[list[str]] = []

set(key_path, value)

function for saving general state (not visualization). This is accessor to set() of inner variable.

Parameters:

• key_path (str) – dot separated path

• value – value to store. The value need to be json serializable.

set_algorithm(key_path, value)

function for saving last algorithm used information. This is accessor to set() of inner variable.

Parameters:

• key_path (str) – dot separated path

• value – value to store. The value need to be json serializable.

set_history(history)

set_project_info(data)

Set project info

set_segmentation_result(result)

property theme_name: str

Name of current theme.

static verify_image(image, silent=True)

Return type:

Union[Image, bool]

class PartSeg.common_backend.base_settings.Color(text)

Bases: object

as_rgb_tuple()

class PartSeg.common_backend.base_settings.ColormapDict(editable_items)

Bases: PartiallyConstDict[Colormap]

Dict for mixing custom colormap with predefined ones

property colormap_added

Signal that colormap is added to dict

property colormap_removed

Signal that colormap is removed form dict

const_item_dict: ClassVar[dict[str, Any]] = {'I Blue': Colormap(colors=ColorArray([[1. , 1. , 1. , 1. ],             [0. , 0.2, 0.8, 1. ]], dtype=float32), name='I Blue', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0., 1.], dtype=float32)), 'I Blue_reversed': Colormap(colors=ColorArray([[0. , 0.2, 0.8, 1. ],             [1. , 1. , 1. , 1. ]], dtype=float32), name='custom', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0., 1.], dtype=float32)), 'I Bordeaux': Colormap(colors=ColorArray([[1. , 1. , 1. , 1. ],             [0.8, 0. , 0.2, 1. ]], dtype=float32), name='I Bordeaux', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0., 1.], dtype=float32)), 'I Bordeaux_reversed': Colormap(colors=ColorArray([[0.8, 0. , 0.2, 1. ],             [1. , 1. , 1. , 1. ]], dtype=float32), name='custom', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0., 1.], dtype=float32)), 'I Forest': Colormap(colors=ColorArray([[1. , 1. , 1. , 1. ],             [0. , 0.6, 0. , 1. ]], dtype=float32), name='I Forest', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0., 1.], dtype=float32)), 'I Forest_reversed': Colormap(colors=ColorArray([[0. , 0.6, 0. , 1. ],             [1. , 1. , 1. , 1. ]], dtype=float32), name='custom', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0., 1.], dtype=float32)), 'I Orange': Colormap(colors=ColorArray([[1.        , 1.        , 1.        , 1.        ],             [1.        , 0.45882353, 0.        , 1.        ]],            dtype=float32), name='I Orange', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0., 1.], dtype=float32)), 'I Orange_reversed': Colormap(colors=ColorArray([[1.        , 0.45882353, 0.        , 1.        ],             [1.        , 1.        , 1.        , 1.        ]],            dtype=float32), name='custom', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0., 1.], dtype=float32)), 'I Purple': Colormap(colors=ColorArray([[1.        , 1.        , 1.        , 1.        ],             [0.45882353, 0.        , 1.        , 1.        ]],            dtype=float32), name='I Purple', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0., 1.], dtype=float32)), 'I Purple_reversed': Colormap(colors=ColorArray([[0.45882353, 0.        , 1.        , 1.        ],             [1.        , 1.        , 1.        , 1.        ]],            dtype=float32), name='custom', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0., 1.], dtype=float32)), 'PiYG': Colormap(colors=ColorArray([[0.5568628 , 0.00392157, 0.32156864, 1.        ],             [0.565321  , 0.00792003, 0.32818148, 1.        ],             [0.57377934, 0.01191849, 0.3347943 , 1.        ],             ...,             [0.16462898, 0.40630525, 0.10049981, 1.        ],             [0.15878509, 0.39923108, 0.09926951, 1.        ],             [0.15294118, 0.39215687, 0.09803922, 1.        ]],            shape=(256, 4), dtype=float32), name='PiYG', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0.        , 0.00392157, 0.00784314, 0.01176471, 0.01568628,        0.01960784, 0.02352941, 0.02745098, 0.03137255, 0.03529412,        0.03921569, 0.04313726, 0.04705882, 0.05098039, 0.05490196,        0.05882353, 0.0627451 , 0.06666667, 0.07058824, 0.07450981,        0.07843138, 0.08235294, 0.08627451, 0.09019608, 0.09411765,        0.09803922, 0.10196079, 0.10588235, 0.10980392, 0.11372549,        0.11764706, 0.12156863, 0.1254902 , 0.12941177, 0.13333334,        0.13725491, 0.14117648, 0.14509805, 0.14901961, 0.15294118,        0.15686275, 0.16078432, 0.16470589, 0.16862746, 0.17254902,        0.1764706 , 0.18039216, 0.18431373, 0.1882353 , 0.19215687,        0.19607843, 0.2       , 0.20392157, 0.20784314, 0.21176471,        0.21568628, 0.21960784, 0.22352941, 0.22745098, 0.23137255,        0.23529412, 0.23921569, 0.24313726, 0.24705882, 0.2509804 ,        0.25490198, 0.25882354, 0.2627451 , 0.26666668, 0.27058825,        0.27450982, 0.2784314 , 0.28235295, 0.28627452, 0.2901961 ,        0.29411766, 0.29803923, 0.3019608 , 0.30588236, 0.30980393,        0.3137255 , 0.31764707, 0.32156864, 0.3254902 , 0.32941177,        0.33333334, 0.3372549 , 0.34117648, 0.34509805, 0.34901962,        0.3529412 , 0.35686275, 0.36078432, 0.3647059 , 0.36862746,        0.37254903, 0.3764706 , 0.38039216, 0.38431373, 0.3882353 ,        0.39215687, 0.39607844, 0.4       , 0.40392157, 0.40784314,        0.4117647 , 0.41568628, 0.41960785, 0.42352942, 0.42745098,        0.43137255, 0.43529412, 0.4392157 , 0.44313726, 0.44705883,        0.4509804 , 0.45490196, 0.45882353, 0.4627451 , 0.46666667,        0.47058824, 0.4745098 , 0.47843137, 0.48235294, 0.4862745 ,        0.49019608, 0.49411765, 0.49803922, 0.5019608 , 0.5058824 ,        0.50980395, 0.5137255 , 0.5176471 , 0.52156866, 0.5254902 ,        0.5294118 , 0.53333336, 0.5372549 , 0.5411765 , 0.54509807,        0.54901963, 0.5529412 , 0.5568628 , 0.56078434, 0.5647059 ,        0.5686275 , 0.57254905, 0.5764706 , 0.5803922 , 0.58431375,        0.5882353 , 0.5921569 , 0.59607846, 0.6       , 0.6039216 ,        0.60784316, 0.6117647 , 0.6156863 , 0.61960787, 0.62352943,        0.627451  , 0.6313726 , 0.63529414, 0.6392157 , 0.6431373 ,        0.64705884, 0.6509804 , 0.654902  , 0.65882355, 0.6627451 ,        0.6666667 , 0.67058825, 0.6745098 , 0.6784314 , 0.68235296,        0.6862745 , 0.6901961 , 0.69411767, 0.69803923, 0.7019608 ,        0.7058824 , 0.70980394, 0.7137255 , 0.7176471 , 0.72156864,        0.7254902 , 0.7294118 , 0.73333335, 0.7372549 , 0.7411765 ,        0.74509805, 0.7490196 , 0.7529412 , 0.75686276, 0.7607843 ,        0.7647059 , 0.76862746, 0.77254903, 0.7764706 , 0.78039217,        0.78431374, 0.7882353 , 0.7921569 , 0.79607844, 0.8       ,        0.8039216 , 0.80784315, 0.8117647 , 0.8156863 , 0.81960785,        0.8235294 , 0.827451  , 0.83137256, 0.8352941 , 0.8392157 ,        0.84313726, 0.84705883, 0.8509804 , 0.85490197, 0.85882354,        0.8627451 , 0.8666667 , 0.87058824, 0.8745098 , 0.8784314 ,        0.88235295, 0.8862745 , 0.8901961 , 0.89411765, 0.8980392 ,        0.9019608 , 0.90588236, 0.9098039 , 0.9137255 , 0.91764706,        0.92156863, 0.9254902 , 0.92941177, 0.93333334, 0.9372549 ,        0.9411765 , 0.94509804, 0.9490196 , 0.9529412 , 0.95686275,        0.9607843 , 0.9647059 , 0.96862745, 0.972549  , 0.9764706 ,        0.98039216, 0.9843137 , 0.9882353 , 0.99215686, 0.99607843,        1.        ], dtype=float32)), 'PiYG_reversed': Colormap(colors=ColorArray([[0.15294118, 0.39215687, 0.09803922, 1.        ],             [0.15878509, 0.39923108, 0.09926951, 1.        ],             [0.16462898, 0.40630525, 0.10049981, 1.        ],             ...,             [0.57377934, 0.01191849, 0.3347943 , 1.        ],             [0.565321  , 0.00792003, 0.32818148, 1.        ],             [0.5568628 , 0.00392157, 0.32156864, 1.        ]],            shape=(256, 4), dtype=float32), name='custom', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0.        , 0.00392157, 0.00784314, 0.01176471, 0.01568627,        0.01960784, 0.02352941, 0.02745098, 0.03137255, 0.03529412,        0.03921568, 0.04313725, 0.04705882, 0.05098039, 0.05490196,        0.05882353, 0.06274509, 0.06666666, 0.07058823, 0.0745098 ,        0.07843137, 0.08235294, 0.0862745 , 0.09019607, 0.09411764,        0.09803921, 0.10196078, 0.10588235, 0.10980392, 0.11372548,        0.11764705, 0.12156862, 0.12549019, 0.12941176, 0.13333333,        0.1372549 , 0.14117646, 0.14509803, 0.1490196 , 0.15294117,        0.15686274, 0.1607843 , 0.16470587, 0.16862744, 0.17254901,        0.17647058, 0.18039215, 0.18431371, 0.18823528, 0.19215685,        0.19607842, 0.19999999, 0.20392156, 0.20784312, 0.2117647 ,        0.21568626, 0.21960783, 0.2235294 , 0.22745097, 0.23137254,        0.2352941 , 0.23921567, 0.24313724, 0.24705881, 0.25098038,        0.25490195, 0.2588235 , 0.26274508, 0.26666665, 0.27058822,        0.2745098 , 0.27843136, 0.28235292, 0.2862745 , 0.29019606,        0.29411763, 0.2980392 , 0.30196077, 0.30588233, 0.3098039 ,        0.31372547, 0.31764704, 0.3215686 , 0.32549018, 0.32941175,        0.3333333 , 0.33725488, 0.34117645, 0.34509802, 0.3490196 ,        0.35294116, 0.35686272, 0.3607843 , 0.36470586, 0.36862743,        0.372549  , 0.37647057, 0.38039213, 0.3843137 , 0.38823527,        0.39215684, 0.3960784 , 0.39999998, 0.40392154, 0.4078431 ,        0.41176468, 0.41568625, 0.41960782, 0.4235294 , 0.42745095,        0.43137252, 0.4352941 , 0.43921566, 0.44313723, 0.4470588 ,        0.45098037, 0.45490193, 0.4588235 , 0.46274507, 0.46666664,        0.4705882 , 0.47450978, 0.47843134, 0.4823529 , 0.48627448,        0.49019605, 0.49411762, 0.4980392 , 0.50196075, 0.5058824 ,        0.5098039 , 0.5137255 , 0.517647  , 0.52156866, 0.52549016,        0.5294118 , 0.5333333 , 0.5372549 , 0.54117644, 0.54509807,        0.5490196 , 0.5529412 , 0.5568627 , 0.56078434, 0.56470585,        0.5686275 , 0.572549  , 0.5764706 , 0.5803921 , 0.58431375,        0.58823526, 0.5921569 , 0.5960784 , 0.6       , 0.60392153,        0.60784316, 0.61176467, 0.6156863 , 0.6196078 , 0.62352943,        0.62745094, 0.6313726 , 0.6352941 , 0.6392157 , 0.6431372 ,        0.64705884, 0.65098035, 0.654902  , 0.6588235 , 0.6627451 ,        0.6666666 , 0.67058825, 0.67450976, 0.6784314 , 0.6823529 ,        0.6862745 , 0.69019604, 0.69411767, 0.6980392 , 0.7019608 ,        0.7058823 , 0.70980394, 0.71372545, 0.7176471 , 0.7215686 ,        0.7254902 , 0.7294117 , 0.73333335, 0.73725486, 0.7411765 ,        0.745098  , 0.7490196 , 0.7529412 , 0.75686276, 0.7607843 ,        0.7647059 , 0.76862746, 0.77254903, 0.7764706 , 0.78039217,        0.78431374, 0.7882353 , 0.7921569 , 0.79607844, 0.8       ,        0.8039216 , 0.80784315, 0.8117647 , 0.8156863 , 0.81960785,        0.8235294 , 0.827451  , 0.83137256, 0.8352941 , 0.8392157 ,        0.84313726, 0.84705883, 0.8509804 , 0.85490197, 0.85882354,        0.8627451 , 0.8666667 , 0.87058824, 0.8745098 , 0.8784314 ,        0.88235295, 0.8862745 , 0.8901961 , 0.89411765, 0.8980392 ,        0.9019608 , 0.90588236, 0.9098039 , 0.9137255 , 0.91764706,        0.92156863, 0.9254902 , 0.92941177, 0.93333334, 0.9372549 ,        0.9411765 , 0.94509804, 0.9490196 , 0.9529412 , 0.95686275,        0.9607843 , 0.9647059 , 0.96862745, 0.972549  , 0.9764706 ,        0.98039216, 0.9843137 , 0.9882353 , 0.99215686, 0.99607843,        1.        ], dtype=float32)), 'blue': Colormap(colors=ColorArray([[0., 0., 0., 1.],             [0., 0., 1., 1.]], dtype=float32), name='blue', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0., 1.], dtype=float32)), 'blue_reversed': Colormap(colors=ColorArray([[0., 0., 1., 1.],             [0., 0., 0., 1.]], dtype=float32), name='custom', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0., 1.], dtype=float32)), 'bop blue': Colormap(colors=ColorArray([[0.        , 0.        , 0.        , 1.        ],             [0.        , 0.        , 0.        , 1.        ],             [0.        , 0.00392157, 0.00392157, 1.        ],             ...,             [0.12156863, 0.6666667 , 0.9607843 , 1.        ],             [0.12156863, 0.67058825, 0.9647059 , 1.        ],             [0.1254902 , 0.6784314 , 0.972549  , 1.        ]],            shape=(256, 4), dtype=float32), name='bop blue', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0.        , 0.00392157, 0.00784314, 0.01176471, 0.01568628,        0.01960784, 0.02352941, 0.02745098, 0.03137255, 0.03529412,        0.03921569, 0.04313726, 0.04705882, 0.05098039, 0.05490196,        0.05882353, 0.0627451 , 0.06666667, 0.07058824, 0.07450981,        0.07843138, 0.08235294, 0.08627451, 0.09019608, 0.09411765,        0.09803922, 0.10196079, 0.10588235, 0.10980392, 0.11372549,        0.11764706, 0.12156863, 0.1254902 , 0.12941177, 0.13333334,        0.13725491, 0.14117648, 0.14509805, 0.14901961, 0.15294118,        0.15686275, 0.16078432, 0.16470589, 0.16862746, 0.17254902,        0.1764706 , 0.18039216, 0.18431373, 0.1882353 , 0.19215687,        0.19607843, 0.2       , 0.20392157, 0.20784314, 0.21176471,        0.21568628, 0.21960784, 0.22352941, 0.22745098, 0.23137255,        0.23529412, 0.23921569, 0.24313726, 0.24705882, 0.2509804 ,        0.25490198, 0.25882354, 0.2627451 , 0.26666668, 0.27058825,        0.27450982, 0.2784314 , 0.28235295, 0.28627452, 0.2901961 ,        0.29411766, 0.29803923, 0.3019608 , 0.30588236, 0.30980393,        0.3137255 , 0.31764707, 0.32156864, 0.3254902 , 0.32941177,        0.33333334, 0.3372549 , 0.34117648, 0.34509805, 0.34901962,        0.3529412 , 0.35686275, 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0.00392157, 0.00784314, 0.01176471, 0.01568628,        0.01960784, 0.02352941, 0.02745098, 0.03137255, 0.03529412,        0.03921569, 0.04313726, 0.04705882, 0.05098039, 0.05490196,        0.05882353, 0.0627451 , 0.06666667, 0.07058824, 0.07450981,        0.07843138, 0.08235294, 0.08627451, 0.09019608, 0.09411765,        0.09803922, 0.10196079, 0.10588235, 0.10980392, 0.11372549,        0.11764706, 0.12156863, 0.1254902 , 0.12941177, 0.13333334,        0.13725491, 0.14117648, 0.14509805, 0.14901961, 0.15294118,        0.15686275, 0.16078432, 0.16470589, 0.16862746, 0.17254902,        0.1764706 , 0.18039216, 0.18431373, 0.1882353 , 0.19215687,        0.19607843, 0.2       , 0.20392157, 0.20784314, 0.21176471,        0.21568628, 0.21960784, 0.22352941, 0.22745098, 0.23137255,        0.23529412, 0.23921569, 0.24313726, 0.24705882, 0.2509804 ,        0.25490198, 0.25882354, 0.2627451 , 0.26666668, 0.27058825,        0.27450982, 0.2784314 , 0.28235295, 0.28627452, 0.2901961 ,        0.29411766, 0.29803923, 0.3019608 , 0.30588236, 0.30980393,        0.3137255 , 0.31764707, 0.32156864, 0.3254902 , 0.32941177,        0.33333334, 0.3372549 , 0.34117648, 0.34509805, 0.34901962,        0.3529412 , 0.35686275, 0.36078432, 0.3647059 , 0.36862746,        0.37254903, 0.3764706 , 0.38039216, 0.38431373, 0.3882353 ,        0.39215687, 0.39607844, 0.4       , 0.40392157, 0.40784314,        0.4117647 , 0.41568628, 0.41960785, 0.42352942, 0.42745098,        0.43137255, 0.43529412, 0.4392157 , 0.44313726, 0.44705883,        0.4509804 , 0.45490196, 0.45882353, 0.4627451 , 0.46666667,        0.47058824, 0.4745098 , 0.47843137, 0.48235294, 0.4862745 ,        0.49019608, 0.49411765, 0.49803922, 0.5019608 , 0.5058824 ,        0.50980395, 0.5137255 , 0.5176471 , 0.52156866, 0.5254902 ,        0.5294118 , 0.53333336, 0.5372549 , 0.5411765 , 0.54509807,        0.54901963, 0.5529412 , 0.5568628 , 0.56078434, 0.5647059 ,        0.5686275 , 0.57254905, 0.5764706 , 0.5803922 , 0.58431375,        0.5882353 , 0.5921569 , 0.59607846, 0.6       , 0.6039216 ,        0.60784316, 0.6117647 , 0.6156863 , 0.61960787, 0.62352943,        0.627451  , 0.6313726 , 0.63529414, 0.6392157 , 0.6431373 ,        0.64705884, 0.6509804 , 0.654902  , 0.65882355, 0.6627451 ,        0.6666667 , 0.67058825, 0.6745098 , 0.6784314 , 0.68235296,        0.6862745 , 0.6901961 , 0.69411767, 0.69803923, 0.7019608 ,        0.7058824 , 0.70980394, 0.7137255 , 0.7176471 , 0.72156864,        0.7254902 , 0.7294118 , 0.73333335, 0.7372549 , 0.7411765 ,        0.74509805, 0.7490196 , 0.7529412 , 0.75686276, 0.7607843 ,        0.7647059 , 0.76862746, 0.77254903, 0.7764706 , 0.78039217,        0.78431374, 0.7882353 , 0.7921569 , 0.79607844, 0.8       ,        0.8039216 , 0.80784315, 0.8117647 , 0.8156863 , 0.81960785,        0.8235294 , 0.827451  , 0.83137256, 0.8352941 , 0.8392157 ,        0.84313726, 0.84705883, 0.8509804 , 0.85490197, 0.85882354,        0.8627451 , 0.8666667 , 0.87058824, 0.8745098 , 0.8784314 ,        0.88235295, 0.8862745 , 0.8901961 , 0.89411765, 0.8980392 ,        0.9019608 , 0.90588236, 0.9098039 , 0.9137255 , 0.91764706,        0.92156863, 0.9254902 , 0.92941177, 0.93333334, 0.9372549 ,        0.9411765 , 0.94509804, 0.9490196 , 0.9529412 , 0.95686275,        0.9607843 , 0.9647059 , 0.96862745, 0.972549  , 0.9764706 ,        0.98039216, 0.9843137 , 0.9882353 , 0.99215686, 0.99607843,        1.        ], dtype=float32)), 'viridis_reversed': Colormap(colors=ColorArray([[0.993248, 0.906157, 0.143936, 1.      ],             [0.983868, 0.904867, 0.136897, 1.      ],             [0.974417, 0.90359 , 0.130215, 1.      ],             ...,             [0.269944, 0.014625, 0.341379, 1.      ],             [0.26851 , 0.009605, 0.335427, 1.      ],             [0.267004, 0.004874, 0.329415, 1.      ]],            shape=(256, 4), dtype=float32), name='custom', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0.        , 0.00392157, 0.00784314, 0.01176471, 0.01568627,        0.01960784, 0.02352941, 0.02745098, 0.03137255, 0.03529412,        0.03921568, 0.04313725, 0.04705882, 0.05098039, 0.05490196,        0.05882353, 0.06274509, 0.06666666, 0.07058823, 0.0745098 ,        0.07843137, 0.08235294, 0.0862745 , 0.09019607, 0.09411764,        0.09803921, 0.10196078, 0.10588235, 0.10980392, 0.11372548,        0.11764705, 0.12156862, 0.12549019, 0.12941176, 0.13333333,        0.1372549 , 0.14117646, 0.14509803, 0.1490196 , 0.15294117,        0.15686274, 0.1607843 , 0.16470587, 0.16862744, 0.17254901,        0.17647058, 0.18039215, 0.18431371, 0.18823528, 0.19215685,        0.19607842, 0.19999999, 0.20392156, 0.20784312, 0.2117647 ,        0.21568626, 0.21960783, 0.2235294 , 0.22745097, 0.23137254,        0.2352941 , 0.23921567, 0.24313724, 0.24705881, 0.25098038,        0.25490195, 0.2588235 , 0.26274508, 0.26666665, 0.27058822,        0.2745098 , 0.27843136, 0.28235292, 0.2862745 , 0.29019606,        0.29411763, 0.2980392 , 0.30196077, 0.30588233, 0.3098039 ,        0.31372547, 0.31764704, 0.3215686 , 0.32549018, 0.32941175,        0.3333333 , 0.33725488, 0.34117645, 0.34509802, 0.3490196 ,        0.35294116, 0.35686272, 0.3607843 , 0.36470586, 0.36862743,        0.372549  , 0.37647057, 0.38039213, 0.3843137 , 0.38823527,        0.39215684, 0.3960784 , 0.39999998, 0.40392154, 0.4078431 ,        0.41176468, 0.41568625, 0.41960782, 0.4235294 , 0.42745095,        0.43137252, 0.4352941 , 0.43921566, 0.44313723, 0.4470588 ,        0.45098037, 0.45490193, 0.4588235 , 0.46274507, 0.46666664,        0.4705882 , 0.47450978, 0.47843134, 0.4823529 , 0.48627448,        0.49019605, 0.49411762, 0.4980392 , 0.50196075, 0.5058824 ,        0.5098039 , 0.5137255 , 0.517647  , 0.52156866, 0.52549016,        0.5294118 , 0.5333333 , 0.5372549 , 0.54117644, 0.54509807,        0.5490196 , 0.5529412 , 0.5568627 , 0.56078434, 0.56470585,        0.5686275 , 0.572549  , 0.5764706 , 0.5803921 , 0.58431375,        0.58823526, 0.5921569 , 0.5960784 , 0.6       , 0.60392153,        0.60784316, 0.61176467, 0.6156863 , 0.6196078 , 0.62352943,        0.62745094, 0.6313726 , 0.6352941 , 0.6392157 , 0.6431372 ,        0.64705884, 0.65098035, 0.654902  , 0.6588235 , 0.6627451 ,        0.6666666 , 0.67058825, 0.67450976, 0.6784314 , 0.6823529 ,        0.6862745 , 0.69019604, 0.69411767, 0.6980392 , 0.7019608 ,        0.7058823 , 0.70980394, 0.71372545, 0.7176471 , 0.7215686 ,        0.7254902 , 0.7294117 , 0.73333335, 0.73725486, 0.7411765 ,        0.745098  , 0.7490196 , 0.7529412 , 0.75686276, 0.7607843 ,        0.7647059 , 0.76862746, 0.77254903, 0.7764706 , 0.78039217,        0.78431374, 0.7882353 , 0.7921569 , 0.79607844, 0.8       ,        0.8039216 , 0.80784315, 0.8117647 , 0.8156863 , 0.81960785,        0.8235294 , 0.827451  , 0.83137256, 0.8352941 , 0.8392157 ,        0.84313726, 0.84705883, 0.8509804 , 0.85490197, 0.85882354,        0.8627451 , 0.8666667 , 0.87058824, 0.8745098 , 0.8784314 ,        0.88235295, 0.8862745 , 0.8901961 , 0.89411765, 0.8980392 ,        0.9019608 , 0.90588236, 0.9098039 , 0.9137255 , 0.91764706,        0.92156863, 0.9254902 , 0.92941177, 0.93333334, 0.9372549 ,        0.9411765 , 0.94509804, 0.9490196 , 0.9529412 , 0.95686275,        0.9607843 , 0.9647059 , 0.96862745, 0.972549  , 0.9764706 ,        0.98039216, 0.9843137 , 0.9882353 , 0.99215686, 0.99607843,        1.        ], dtype=float32)), 'yellow': Colormap(colors=ColorArray([[0., 0., 0., 1.],             [1., 1., 0., 1.]], dtype=float32), name='yellow', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0., 1.], dtype=float32)), 'yellow_reversed': Colormap(colors=ColorArray([[1., 1., 0., 1.],             [0., 0., 0., 1.]], dtype=float32), name='custom', interpolation=<ColormapInterpolationMode.LINEAR: 'linear'>, controls=array([0., 1.], dtype=float32))}

Dict with non removable elements

class PartSeg.common_backend.base_settings.ImageSettings

Bases: QObject

Base class for all PartSeg settings. Keeps information about current Image.

property additional_layers: dict[str, AdditionalLayerDescription]

additional_layers_changed

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

property channels

components_mask()

property full_segmentation

property has_channels

property image

image_changed(Image)

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

image_channel_count_changed(int)

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

property image_path

image_path_changed(str)

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

property image_shape

property image_spacing

Image.spacing() proxy

image_spacing_changed

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

is_image_2d()

Image.is_2d() proxy

property noise_remove_image_part

property roi: ndarray

current roi

roi_changed(ROIInfo)

Signal emitted when roi has changed

roi_clean

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

property roi_info: ROIInfo

property segmentation: ndarray

current roi

property segmentation_info: ROIInfo

set_parent(parent)

property sizes

class PartSeg.common_backend.base_settings.LabelColorDict(editable_items)

Bases: PartiallyConstDict[list]

Dict for mixing custom label colors with predefined ones`

const_item_dict: ClassVar[dict[str, Any]] = {'default': [[0, 205, 0], [0, 0, 255], [0, 255, 255], [255, 0, 255], [255, 127, 0], [0, 100, 0], [138, 43, 226], [139, 35, 35], [0, 0, 128], [139, 139, 0], [255, 62, 150], [139, 76, 57], [0, 134, 139], [205, 104, 57], [191, 62, 255], [0, 139, 69], [199, 21, 133], [205, 55, 0], [32, 178, 170], [106, 90, 205], [255, 20, 147], [69, 139, 116], [72, 118, 255], [205, 79, 57], [0, 0, 205], [139, 34, 82], [139, 0, 139], [238, 130, 238], [139, 0, 0], [255, 0, 0]]}

Non removable items for this dict. Current value is default_label_dict

get_array(key)

Get labels as numpy array

Return type:

ndarray

class PartSeg.common_backend.base_settings.SaveSettingsDescription(file_name, values)

Bases: NamedTuple

file_name: str

Alias for field number 0

values: Union[dict, ProfileDict]

Alias for field number 1

exception PartSeg.common_backend.base_settings.SwapTimeStackException

Bases: Exception

Exception which inform that current image shape is not supported, but can be if time and stack axes were swapped

exception PartSeg.common_backend.base_settings.TimeAndStackException

Bases: Exception

Exception which inform that current image has both time and stack dat which is not supported

class PartSeg.common_backend.base_settings.ViewSettings

Bases: ImageSettings

property available_colormaps

change_profile(name)

property chosen_colormap

Sequence of selected colormap to be available in dropdown

chosen_colormap_change(name, visibility)

colormap_changes

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

connect_channel_colormap_name(view, fun)

connect_to_profile(key_path, callback)

property current_labels

Current labels scheme for marking ROI

get_channel_colormap_name(view, num, default=None)

Return type:

str

get_channel_info(view, num, default=None)

Return type:

str

get_from_profile(key_path, default=None)

Function for getting information used in visualization. This is accessor to get() of inner variable.

Parameters:

• key_path – dot separated path

• default – default value if key is missed

get_style_sheet()

QSS style sheet for current theme.

property label_colors

labels_changed

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

profile_data_changed(str, object)

Signal about changes in stored data (set with set_in_profile)

set_channel_colormap_name(view, num, value)

set_channel_info(view, num, value)

set_in_profile(key_path, value)

Function for saving information used in visualization. This is accessor to set() of inner variable.

Parameters:

• key_path – dot separated path

• value – value to store. The value need to be json serializable.

property style_sheet

property theme

Theme as structure.

theme_changed

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

static theme_list()

Sequence of available themes

property theme_name: str

Name of current theme.

PartSeg.common_backend.except_hook module

PartSeg.common_backend.except_hook.my_excepthook(type_, value, trace_back)

Custom excepthook. Close application on KeyboardInterrupt.

If PartSeg.state_store.always_report is set then just sent report using sentry. otherwise show dialog with information about error and ask user if he wants to send report using show_error().

PartSeg.common_backend.except_hook.show_error(error=None)

For SegmentationLimitException and TiffFileException show dialog with information about problem.

For other exceptions show ErrorDialog dialog with information about error that allow to report it.

Parameters:

error – exception to show

PartSeg.common_backend.except_hook.show_warning(header=None, text=None, exception=None)

Show warning QMessageBox

This function is to ensure creation warning dialog in main thread.

PartSeg.common_backend.load_backup module

PartSeg.common_backend.load_backup.import_config()

Check if settings folder for current version already exists.

Otherwise, when settings for previous PartSeg version exists, ask user if he would to import settings from the newest one.

PartSeg.common_backend.partially_const_dict module

class PartSeg.common_backend.partially_const_dict.PartiallyConstDict(editable_items)

Base class for creating dict to mixin predefined and user defined variables.

const_item_dict: ClassVar[dict[str, Any]] = {}

Dict with non removable elements

get_position(key)

Get item position as unique int. For sorting purpose

Raises:

KeyError – if element not in dict

Return type:

int

item_added(object)

Signal with item added to dict

item_removed(object)

Signal with item remove from dict

PartSeg.common_backend.progress_thread module

class PartSeg.common_backend.progress_thread.ExecuteFunctionThread(fun, args=None, kwargs=None)

Bases: ProgressTread

Generic Thread to execute

run(self)

class PartSeg.common_backend.progress_thread.ProgressTread

Bases: QThread

error_signal(Exception)

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

info_function(label, val)

range_changed(int, int)

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

step_changed(int)

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

PartSeg.common_backend.segmentation_thread module

class PartSeg.common_backend.segmentation_thread.SegmentationThread(algorithm)

Bases: QThread

Method to run calculation task in separated Thread. This allows to not freeze main window. To get info if calculation is done connect to finished.

clean()

clean cache if thread is running. Call SegmentationAlgorithm.clean() otherwise. :

exception_occurred(Exception)

Signal emitted when some exception occur during calculation.

execution_done(ROIExtractionResult)

Signal contains result of segmentation algorithm. Emitted if calculation ends without exception and SegmentationAlgorithm.calculation_run() return not None result.

finished_task()

Called on calculation finished. Check if cache is not empty. In such case start calculation again with new parameters.

get_info_text()

Proxy for SegmentationAlgorithm.get_info_text().

progress_signal(str, int)

Signal with information about progress. This is proxy for SegmentationAlgorithm.calculation_run() report_fun parameter`

run()

the calculation are done here

set_image(image)

check if calculation is running. If yes then cache parameters until it finish, otherwise call SegmentationAlgorithm.set_image() :type image: :param image: image to be set

set_mask(mask)

check if calculation is running. If yes then cache parameters until it finish, otherwise call SegmentationAlgorithm.set_mask() :type mask: :param mask: mask to be set

set_parameters(*args, **kwargs)

check if calculation is running. If yes then cache parameters until it finish, otherwise call SegmentationAlgorithm.set_parameters()

start(priority=Priority.InheritPriority)

If calculation is running remember to restart it with new parameters.

Otherwise start immediately.