PartSeg.common_backend package

Module contents

This module contains non gui Qt based components

PartSeg.common_backend.napari_get_settings(path=None)[source]
Return type

NapariSettings

Submodules

PartSeg.common_backend.abstract_class module

class PartSeg.common_backend.abstract_class.QtMeta(name, bases, namespace, **kwargs)[source]

Bases: sip.wrappertype, abc.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)[source]

Bases: argparse.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)[source]

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

PartSeg.common_backend.base_argparser.napari_image_repr(image)[source]
Return type

str

PartSeg.common_backend.base_argparser.proper_path(val)[source]

Check if val is proper path in current system

Raises

argparse.ArgumentTypeError – on validation error

PartSeg.common_backend.base_argparser.proper_suffix(val)[source]

check if val contains only alphanumeric characters

Raises

argparse.ArgumentTypeError – on validation error

PartSeg.common_backend.base_argparser.safe_repr(val)[source]

PartSeg.common_backend.base_settings module

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

Bases: PartSeg.common_backend.base_settings.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)[source]
Return type

None

add_last_files(file_path, load_method)[source]
add_last_files_multiple(file_paths, load_method)[source]
add_load_files_history(file_path, load_method)[source]
add_path_history(dir_path)[source]

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)[source]
connect_(key_path, callback)[source]
dump(folder_path=None)[source]

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)[source]
get(key_path, default=None)[source]

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)[source]

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()[source]
Return type

List[HistoryElement]

get_last_files()[source]
Return type

List[Tuple[Tuple[Union[str, Path], ...], str]]

get_last_files_multiple()[source]
Return type

List[Tuple[Tuple[Union[str, Path], ...], str]]

get_path_history()[source]

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()[source]

Get all information needed to save project

Return type

ProjectInfoBase

get_save_list()[source]

List of files in which program save the state.

Return type

List[SaveSettingsDescription]

history_current_element()[source]
Return type

HistoryElement

history_next_element()[source]
Return type

HistoryElement

history_pop()[source]
Return type

Optional[HistoryElement]

history_redo_clean()[source]
Return type

None

history_redo_size()[source]
Return type

int

history_size()[source]
Return type

int

json_encoder_class

alias of PartSegCore.json_hooks.PartSegEncoder

load(folder_path=None)[source]

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
property points
points_changed
request_load_files(list)

Signal mask changed signal

save_locations_keys: ClassVar[List[str]] = []
set(key_path, value)[source]

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)[source]

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)[source]
set_project_info(data)[source]

Set project info

set_segmentation_result(result)[source]
property theme_name: str

Name of current theme.

Return type

str

static verify_image(image, silent=True)[source]
Return type

Union[Image, bool]

class PartSeg.common_backend.base_settings.Color(text)[source]

Bases: object

as_rgb_tuple()[source]
class PartSeg.common_backend.base_settings.ColormapDict(editable_items)[source]

Bases: PartSeg.common_backend.partially_const_dict.PartiallyConstDict[napari.utils.colormaps.colormap.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=array([[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=array([[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=array([[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=array([[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=array([[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=array([[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=array([[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=array([[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=array([[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=array([[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=array([[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.        ]], 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=array([[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.        ]], 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=array([[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=array([[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=array([[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.        ]], 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, 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 , 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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': Colormap(colors=array([[0.267004, 0.004874, 0.329415, 1.      ],        [0.26851 , 0.009605, 0.335427, 1.      ],        [0.269944, 0.014625, 0.341379, 1.      ],        ...,        [0.974417, 0.90359 , 0.130215, 1.      ],        [0.983868, 0.904867, 0.136897, 1.      ],        [0.993248, 0.906157, 0.143936, 1.      ]], dtype=float32), name='viridis', 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)), 'viridis_reversed': Colormap(colors=array([[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.      ]], 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=array([[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=array([[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[source]

Bases: QObject

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

property additional_layers: Dict[str, PartSegCore.project_info.AdditionalLayerDescription]
Return type

Dict[str, AdditionalLayerDescription]

additional_layers_changed
property channels
components_mask()[source]
property full_segmentation
property has_channels
property image
image_changed(Image)
image_channel_count_changed(int)
property image_path
image_path_changed(str)
property image_shape
property image_spacing

Image.spacing() proxy

image_spacing_changed
is_image_2d()[source]

Image.is_2d() proxy

property noise_remove_image_part
property roi: numpy.ndarray

current roi

Return type

ndarray

roi_changed(ROIInfo)

Signal emitted when roi has changed

roi_clean
property roi_info: PartSegCore.roi_info.ROIInfo
Return type

ROIInfo

property segmentation: numpy.ndarray

current roi

Return type

ndarray

property segmentation_info: PartSegCore.roi_info.ROIInfo
Return type

ROIInfo

set_parent(parent)[source]
property sizes
class PartSeg.common_backend.base_settings.LabelColorDict(editable_items)[source]

Bases: PartSeg.common_backend.partially_const_dict.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)[source]

Get labels as numpy array

Return type

ndarray

class PartSeg.common_backend.base_settings.SaveSettingsDescription(file_name, values)[source]

Bases: NamedTuple

file_name: str

Alias for field number 0

values: Union[dict, PartSegCore.utils.ProfileDict]

Alias for field number 1

exception PartSeg.common_backend.base_settings.SwapTimeStackException[source]

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[source]

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[source]

Bases: PartSeg.common_backend.base_settings.ImageSettings

property available_colormaps
change_profile(name)[source]
property chosen_colormap

Sequence of selected colormap to be available in dropdown

chosen_colormap_change(name, visibility)[source]
colormap_changes
connect_channel_colormap_name(view, fun)[source]
connect_to_profile(key_path, callback)[source]
property current_labels

Current labels scheme for marking ROI

get_channel_colormap_name(view, num, default=None)[source]
Return type

str

get_channel_info(view, num, default=None)[source]
Return type

str

get_from_profile(key_path, default=None)[source]

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()[source]

QSS style sheet for current theme.

property label_colors
labels_changed
profile_data_changed(str, object)

Signal about changes in stored data (set with set_in_profile)

set_channel_colormap_name(view, num, value)[source]
set_channel_info(view, num, value)[source]
set_in_profile(key_path, value)[source]

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
static theme_list()[source]

Sequence of available themes

property theme_name: str

Name of current theme.

Return type

str

PartSeg.common_backend.except_hook module

PartSeg.common_backend.except_hook.my_excepthook(type_, value, trace_back)[source]

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)[source]

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)[source]

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()[source]

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)[source]

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)[source]

Get item position as unique int. For soring 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 fom dict

PartSeg.common_backend.progress_thread module

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

Bases: PartSeg.common_backend.progress_thread.ProgressTread

Generic Thread to execute

run(self)[source]
class PartSeg.common_backend.progress_thread.ProgressTread[source]

Bases: QThread

error_signal(Exception)
info_function(label, val)[source]
ProgressTread.range_changed(int, int)
step_changed(int)

PartSeg.common_backend.segmentation_thread module

class PartSeg.common_backend.segmentation_thread.SegmentationThread(algorithm)[source]

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()[source]

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()[source]

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

get_info_text()[source]

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()[source]

the calculation are done here

set_image(image)[source]

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

set_mask(mask)[source]

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

set_parameters(*args, **kwargs)[source]

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

start(priority=7)[source]

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

Otherwise start immediately.