pocketutils.biochem.multiwell_plate_rois.PlateRois._get_roi_coordinates() - Code Metrics - Inspection of "feat: deprecated code; fixed from_toml; added logu..." - dmyersturnbull/pocketutils - Measure and Improve Code Quality continuously with Scrutinizer

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Push — main ( 29adcf...6c3df6 )

by Douglas

created 2021-10-05 01:43 UTC

PlateRois._get_roi_coordinates() B

↳ Parent: pocketutils.biochem.multiwell_plate_rois

Complexity

Conditions

Size

Total Lines	28
Code Lines	25

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	7
eloc	25
nop	4
dl	0
loc	28
rs	7.8799
c	0
b	0
f	0

import typing

from dataclasses import dataclass
from enum import Enum
from typing import Dict

from pocketutils.core.exceptions import OutOfRangeError, ErrorUtils


class Edge(Enum):

    left = 1
    right = 2
    top = 3
    bottom = 4


class Axis(Enum):

    horizontal = 1
    vertical = 2


@ErrorUtils.args(edge=Edge, axis=Axis)

class RoiError(OutOfRangeError):
    """The ROI is invalid."""


@dataclass(frozen=True, order=True)

class WellRoi:
    row: int
    column: int
    x0: int

    y0: int

    x1: int

    y1: int


    def __post_init__(self):
        if self.row < 0:
            raise OutOfRangeError(f"Row ({self.row}) < 0", value=self.row)
        if self.column < 0:
            raise OutOfRangeError(f"Column ({self.column}) < 0", value=self.column)
        if self.x0 < 0:
            raise RoiError(f"x0 ({self.x0}) < 0", edge=Edge.left)
        if self.y0 < 0:
            raise RoiError(f"y0 ({self.y0}) < 0", edge=Edge.top)
        if self.x0 >= self.x1:
            raise RoiError(f"x0 ({self.x0}) >= x1 ({self.x1})", axis=Axis.horizontal)
        if self.y0 >= self.y1:
            raise RoiError(f"y0 ({self.y0}) >= y1 ({self.y1})", axis=Axis.vertical)

    def __repr__(self) -> str:
        return f"{self.row},{self.column}=({self.x0},{self.y0})→({self.x1},{self.y1})"

    def __str__(self):
        return repr(self)


@dataclass(frozen=True, repr=True, order=True)

class PlateRois:
    n_rows: int
    n_columns: int
    image_roi: WellRoi
    top_left_roi: WellRoi
    padx: float
    pady: float

    @property
    def well_rois(self):

        return self._get_roi_coordinates(self.top_left_roi, self.padx, self.pady)

    def __iter__(self):
        return iter(self.well_rois.keys())

    def __len__(self):
        return len(self.well_rois)

    def __getitem__(self, item):
        try:
            return self.well_rois[item[0], item[1]]
        except (IndexError, AttributeError):
            raise TypeError("Must look up well ROIs by (row, column) tuple indices.")

    def _get_roi_coordinates(
        self, top_left_roi: WellRoi, padx: float, pady: float

    ) -> Dict[typing.Tuple[int, int], WellRoi]:
        tl = top_left_roi

        width = top_left_roi.x1 - top_left_roi.x0
        height = top_left_roi.y1 - top_left_roi.y0
        wells_x_edge = tl.x0 + self.n_columns * width + (self.n_columns - 1) * padx
        wells_y_edge = tl.y0 + self.n_rows * height + (self.n_rows - 1) * pady
        # make sure the wells don't extend outside the image bounds
        if tl.x0 < self.image_roi.x0:
            raise RoiError(f"{tl.x0} < {self.image_roi.x0}", edge=Edge.left)
        if wells_x_edge > self.image_roi.x1:
            raise RoiError(f"{wells_x_edge} < {self.image_roi.x1}", edge=Edge.right)
        if tl.y0 < self.image_roi.y0:
            raise RoiError(f"{tl.y0} < {self.image_roi.y0}", edge=Edge.top)
        if wells_y_edge > self.image_roi.y1:
            raise RoiError(f"{wells_y_edge} > {self.image_roi.y1}", edge=Edge.bottom)
        # now build
        rois = {}
        x = tl.x0

        y = tl.y0

        for row in range(0, self.n_rows):
            for column in range(0, self.n_columns):
                rois[(row, column)] = WellRoi(row, column, x, y, x + width, y + height)
                x += width + padx

            y += height + pady

            x = tl.x0

        return rois


__all__ = ["WellRoi", "PlateRois"]


1			import typing
			0 ignored issues – show introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Missing module docstring Loading history...
2			from dataclasses import dataclass
3			from enum import Enum
4			from typing import Dict
5
6			from pocketutils.core.exceptions import OutOfRangeError, ErrorUtils
7
8
9			class Edge(Enum):
			0 ignored issues – show introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
10			left = 1
11			right = 2
12			top = 3
13			bottom = 4
14
15
16			class Axis(Enum):
			0 ignored issues – show introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
17			horizontal = 1
18			vertical = 2
19
20
21			@ErrorUtils.args(edge=Edge, axis=Axis)
			0 ignored issues – show best-practice introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Too many ancestors (8/7) Loading history...
22			class RoiError(OutOfRangeError):
23			"""The ROI is invalid."""
24
25
26			@dataclass(frozen=True, order=True)
			0 ignored issues – show introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
27			class WellRoi:
28			row: int
29			column: int
30			x0: int
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 07:52 UTC by Report Bug Copy Issue Report Attribute name "x0" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
31			y0: int
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Attribute name "y0" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
32			x1: int
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Attribute name "x1" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
33			y1: int
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Attribute name "y1" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
34
35			def __post_init__(self):
36			if self.row < 0:
37			raise OutOfRangeError(f"Row ({self.row}) < 0", value=self.row)
38			if self.column < 0:
39			raise OutOfRangeError(f"Column ({self.column}) < 0", value=self.column)
40			if self.x0 < 0:
41			raise RoiError(f"x0 ({self.x0}) < 0", edge=Edge.left)
42			if self.y0 < 0:
43			raise RoiError(f"y0 ({self.y0}) < 0", edge=Edge.top)
44			if self.x0 >= self.x1:
45			raise RoiError(f"x0 ({self.x0}) >= x1 ({self.x1})", axis=Axis.horizontal)
46			if self.y0 >= self.y1:
47			raise RoiError(f"y0 ({self.y0}) >= y1 ({self.y1})", axis=Axis.vertical)
48
49			def __repr__(self) -> str:
50			return f"{self.row},{self.column}=({self.x0},{self.y0})→({self.x1},{self.y1})"
51
52			def __str__(self):
53			return repr(self)
54
55
56			@dataclass(frozen=True, repr=True, order=True)
			0 ignored issues – show introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
57			class PlateRois:
58			n_rows: int
59			n_columns: int
60			image_roi: WellRoi
61			top_left_roi: WellRoi
62			padx: float
63			pady: float
64
65			@property
66			def well_rois(self):
			0 ignored issues – show introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
67			return self._get_roi_coordinates(self.top_left_roi, self.padx, self.pady)
68
69			def __iter__(self):
70			return iter(self.well_rois.keys())
71
72			def __len__(self):
73			return len(self.well_rois)
74
75			def __getitem__(self, item):
76			try:
77			return self.well_rois[item[0], item[1]]
78			except (IndexError, AttributeError):
79			raise TypeError("Must look up well ROIs by (row, column) tuple indices.")
80
81			def _get_roi_coordinates(
82			self, top_left_roi: WellRoi, padx: float, pady: float
			0 ignored issues – show Coding Style introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
83			) -> Dict[typing.Tuple[int, int], WellRoi]:
84			tl = top_left_roi
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Variable name "tl" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
85			width = top_left_roi.x1 - top_left_roi.x0
86			height = top_left_roi.y1 - top_left_roi.y0
87			wells_x_edge = tl.x0 + self.n_columns * width + (self.n_columns - 1) * padx
88			wells_y_edge = tl.y0 + self.n_rows * height + (self.n_rows - 1) * pady
89			# make sure the wells don't extend outside the image bounds
90			if tl.x0 < self.image_roi.x0:
91			raise RoiError(f"{tl.x0} < {self.image_roi.x0}", edge=Edge.left)
92			if wells_x_edge > self.image_roi.x1:
93			raise RoiError(f"{wells_x_edge} < {self.image_roi.x1}", edge=Edge.right)
94			if tl.y0 < self.image_roi.y0:
95			raise RoiError(f"{tl.y0} < {self.image_roi.y0}", edge=Edge.top)
96			if wells_y_edge > self.image_roi.y1:
97			raise RoiError(f"{wells_y_edge} > {self.image_roi.y1}", edge=Edge.bottom)
98			# now build
99			rois = {}
100			x = tl.x0
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Variable name "x" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
101			y = tl.y0
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Variable name "y" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
102			for row in range(0, self.n_rows):
103			for column in range(0, self.n_columns):
104			rois[(row, column)] = WellRoi(row, column, x, y, x + width, y + height)
105			x += width + padx
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Variable name "x" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
106			y += height + pady
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Variable name "y" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
107			x = tl.x0
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 05:25 UTC by Report Bug Copy Issue Report Variable name "x" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
108			return rois
109
110
111			__all__ = ["WellRoi", "PlateRois"]
112

dmyersturnbull / pocketutils

Push — main ( 29adcf...6c3df6 )

PlateRois._get_roi_coordinates() B

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