mandos.analysis._plot_utils.VizResources._get_named_cmaps() - Code Metrics - Inspection of "fix: small" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Push — main ( 37036d...9cce85 )

by Douglas

created 2021-09-09 01:52 UTC

VizResources._get_named_cmaps() A

↳ Parent: mandos.analysis._plot_utils

Complexity

Conditions

Size

Total Lines	14
Code Lines	13

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	3
eloc	13
nop	1
dl	0
loc	14
rs	9.75
c	0
b	0
f	0

"""


"""
from __future__ import annotations

import enum
from pathlib import Path
from typing import Union, Optional, Tuple, Mapping, Any, Generator, Sequence, Set

import numpy as np

import pandas as pd

from matplotlib import pyplot as plt

from matplotlib.colors import LinearSegmentedColormap, Colormap, ListedColormap, to_hex

from matplotlib.figure import Figure

from pocketutils.core.dot_dict import NestedDotDict

from pocketutils.tools.common_tools import CommonTools


# noinspection PyProtectedMember
from seaborn.palettes import SEABORN_PALETTES

from typeddfs import TypedDfs


from mandos.model.utils.setup import logger

from mandos.model.utils import CleverEnum
from mandos.model.utils.misc_utils import MiscUtils
from mandos.model.utils.resources import MandosResources

try:
    import seaborn as sns
    from matplotlib.axes import Axes

    from matplotlib.figure import Figure

except ImportError:
    sns = None
    Axes = None
    Figure = None


class DataType(CleverEnum):

    qualitative = enum.auto()
    sequential = enum.auto()
    divergent = enum.auto()


class VizResources:

    def __init__(self):
        self.override_settings = MandosResources.json_dict("viz", "style_override.json")
        self.dims = MandosResources.json_dict("viz", "page_dims.json")
        palettes = MandosResources.json_dict("viz", "palettes.json")
        self.named_palettes = palettes["named"]
        self.default_palettes = palettes["defaults"]
        self.named_cmaps = self._get_named_cmaps()

    def _get_named_cmaps(self) -> Mapping[str, Colormap]:
        cmaps = {}
        for name, cmap in self.named_palettes.items():
            cmap = NestedDotDict(cmap)
            seq = cmap.req_list_as("sequence", str)
            seq = [to_hex(c) for c in seq]
            cat = cmap.req_as("categorical", bool)
            if cat:
                cmaps[name] = ListedColormap(seq)
            else:
                nan, under, over = cmap.get("nan"), cmap.get("under"), cmap.get("over")
                cmap = LinearSegmentedColormap.from_list(name, seq)
                cmap.set_extremes(bad=nan, under=under, over=over)
        return cmaps


VIZ_RESOURCES = VizResources()


class MandosPlotStyling:

    @classmethod
    def list_named_palettes(cls) -> Set[str]:

        return {
            *VIZ_RESOURCES.named_palettes.keys(),
            *SEABORN_PALETTES,
            *plt.colormaps(),
        }

    @classmethod
    def choose_palette(

        cls,

        data: pd.DataFrame,

        col: Optional[str],

        palette: Optional[str],

    ) -> Union[None, Colormap, Mapping[str, str]]:
        if col is None:
            return None
        unique = data[col].unique()
        dtype = cls.guess_data_type(data)
        if palette is None:
            palette = cls.get_palette(None, dtype)
        if dtype is DataType.qualitative:
            if not isinstance(palette, ListedColormap):
                raise TypeError(f"{palette} is not a valid choice for {dtype}")
            if len(unique) > len(palette.colors):
                raise ValueError(
                    f"Palette (N={len(palette.colors)}) too small for {len(unique)} items"
                )
            return {i: j for i, j in CommonTools.zip_strict(unique, map(to_hex, palette.colors))}

        return palette

    @classmethod
    def get_palette(cls, name: Optional[str], data_type: Union[DataType, str]) -> Colormap:

        data_type = DataType.of(data_type)
        if name is None:
            name = VIZ_RESOURCES.default_palettes[data_type.name]
        if name in VIZ_RESOURCES.named_cmaps:
            return VIZ_RESOURCES.named_cmaps[name]
        return sns.color_palette(name, as_cmap=True)

    @classmethod
    def guess_data_type(cls, data: Sequence[Union[str, float]]) -> DataType:

        numerical = cls._to_numerical(data)
        if numerical is None:
            return DataType.qualitative
        is_divergent = cls._are_floats_divergent(data)
        if is_divergent:
            return DataType.divergent
        return DataType.sequential

    @classmethod
    def _to_colors(cls, data: Sequence[Union[float, str]]) -> Optional[Sequence[str]]:
        if not all((isinstance(d, str)) for d in data):
            return None
        try:
            return [to_hex(c) for c in data]
        except ValueError:
            return None

    @classmethod
    def _to_numerical(cls, data: Sequence[Union[str, float]]) -> Optional[Sequence[float]]:

        try:
            [float(d) for d in data]
        except ValueError:
            return None

    @classmethod
    def _are_floats_divergent(cls, data: Sequence[float]):
        signs = {np.sign(d) for d in data if d != 0 and not np.isnan(d) and not np.isinf(d)}
        return len(signs) == 2

    @classmethod
    def context(
        cls, style: Union[None, str, Path], kwargs: Optional[Mapping[str, Any]]

    ) -> Generator[None, None, None]:
        """
        Override these from the default style.
        This will be called once, at startup.
        """
        new_kwargs = dict(VIZ_RESOURCES.override_settings["allow_change"])
        if kwargs is not None:
            new_kwargs.update(kwargs)
        with plt.rc_context(new_kwargs, style):
            yield

    @classmethod
    def fig_width_and_height(cls, size: str) -> Tuple[float, float]:

        if size is None:
            return plt.rcParams["figure.figsize"]
        axis_to_str = {
            i: d.strip() for i, d in enumerate(size.replace(" × ", " by ").split(" by "))
        }
        try:
            default_inch = plt.rcParams["figure.figsize"]
            width = cls._to_inch(axis_to_str.get(0), VIZ_RESOURCES.dims["widths"], default_inch[0])
            height = cls._to_inch(
                axis_to_str.get(1), VIZ_RESOURCES.dims["heights"], default_inch[1]
            )
        except ValueError:
            raise ValueError(f"Strange --size format in '{size}'")
        return width, height

    @classmethod
    def _to_inch(

        cls, s: Optional[str], standards: Mapping[str, float], default_inch: float

    ) -> float:
        if s is None or len(s) == "":
            return default_inch
        try:
            return float(s)
        except ValueError:
            pass
        x = standards.get(s, s)

        return MiscUtils.canonicalize_quantity(x, "[length]").to("inch").magnitude


class MandosPlotUtils:

    @classmethod
    def save(cls, figure: Figure, path: Path) -> None:

        path.parent.mkdir(parents=True, exist_ok=True)
        figure.savefig(str(path))
        figure.clear()


CompoundStyleDf = (
    TypedDfs.typed("CompoundStyleDf").require("inchikey", dtype=str).strict(cols=False).secure()
).build()

PredicateObjectStyleDf = (
    TypedDfs.typed("PredicateObjectStyleDf")
    .require("predicate", "object", dtype=str)
    .strict(cols=False)
    .secure()
).build()

PhiPsiStyleDf = (
    TypedDfs.typed("PhiPsiStyleDf").require("phi", "psi", dtype=str).strict(cols=False).secure()
).build()


__all__ = [
    "sns",
    "plt",
    "Figure",
    "Axes",
    "MandosPlotStyling",
    "MandosPlotUtils",
    "CompoundStyleDf",
    "PredicateObjectStyleDf",
    "VIZ_RESOURCES",
]


1			"""
			0 ignored issues – show Documentation introduced 2021-08-02 23:39 UTC by Report Bug Copy Issue Report Empty module docstring Loading history...
2
3			"""
4			from __future__ import annotations
5
6			import enum
7			from pathlib import Path
8			from typing import Union, Optional, Tuple, Mapping, Any, Generator, Sequence, Set
9
10			import numpy as np
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Unable to import 'numpy' Loading history...
11			import pandas as pd
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Unable to import 'pandas' Loading history...
12			from matplotlib import pyplot as plt
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Unable to import 'matplotlib' Loading history...
13			from matplotlib.colors import LinearSegmentedColormap, Colormap, ListedColormap, to_hex
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Unable to import 'matplotlib.colors' Loading history...
14			from matplotlib.figure import Figure
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Unable to import 'matplotlib.figure' Loading history...
15			from pocketutils.core.dot_dict import NestedDotDict
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.core.dot_dict' Loading history...
16			from pocketutils.tools.common_tools import CommonTools
			0 ignored issues – show introduced 2021-09-09 01:56 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.tools.common_tools' Loading history...
17
18			# noinspection PyProtectedMember
19			from seaborn.palettes import SEABORN_PALETTES
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Unable to import 'seaborn.palettes' Loading history...
20			from typeddfs import TypedDfs
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Unable to import 'typeddfs' Loading history...
21
22			from mandos.model.utils.setup import logger
			0 ignored issues – show Unused Code introduced 2021-09-09 01:56 UTC by Report Bug Copy Issue Report Unused logger imported from mandos.model.utils.setup Loading history...
23			from mandos.model.utils import CleverEnum
24			from mandos.model.utils.misc_utils import MiscUtils
25			from mandos.model.utils.resources import MandosResources
26
27			try:
28			import seaborn as sns
29			from matplotlib.axes import Axes
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Imports from package matplotlib are not grouped Loading history...
30			from matplotlib.figure import Figure
			0 ignored issues – show Unused Code introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report The import `Figure` was already done on line 14. You should be able to remove this line. Loading history...
31			except ImportError:
32			sns = None
33			Axes = None
34			Figure = None
35
36
37			class DataType(CleverEnum):
			0 ignored issues – show introduced 2021-08-02 23:39 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
38			qualitative = enum.auto()
39			sequential = enum.auto()
40			divergent = enum.auto()
41
42
43			class VizResources:
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
44			def __init__(self):
45			self.override_settings = MandosResources.json_dict("viz", "style_override.json")
46			self.dims = MandosResources.json_dict("viz", "page_dims.json")
47			palettes = MandosResources.json_dict("viz", "palettes.json")
48			self.named_palettes = palettes["named"]
49			self.default_palettes = palettes["defaults"]
50			self.named_cmaps = self._get_named_cmaps()
51
52			def _get_named_cmaps(self) -> Mapping[str, Colormap]:
53			cmaps = {}
54			for name, cmap in self.named_palettes.items():
55			cmap = NestedDotDict(cmap)
56			seq = cmap.req_list_as("sequence", str)
57			seq = [to_hex(c) for c in seq]
58			cat = cmap.req_as("categorical", bool)
59			if cat:
60			cmaps[name] = ListedColormap(seq)
61			else:
62			nan, under, over = cmap.get("nan"), cmap.get("under"), cmap.get("over")
63			cmap = LinearSegmentedColormap.from_list(name, seq)
64			cmap.set_extremes(bad=nan, under=under, over=over)
65			return cmaps
66
67
68			VIZ_RESOURCES = VizResources()
69
70
71			class MandosPlotStyling:
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
72			@classmethod
73			def list_named_palettes(cls) -> Set[str]:
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
74			return {
75			*VIZ_RESOURCES.named_palettes.keys(),
76			*SEABORN_PALETTES,
77			*plt.colormaps(),
78			}
79
80			@classmethod
81			def choose_palette(
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
82			cls,
			0 ignored issues – show Coding Style introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
83			data: pd.DataFrame,
			0 ignored issues – show Coding Style introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
84			col: Optional[str],
			0 ignored issues – show Coding Style introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
85			palette: Optional[str],
			0 ignored issues – show Coding Style introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
86			) -> Union[None, Colormap, Mapping[str, str]]:
87			if col is None:
88			return None
89			unique = data[col].unique()
90			dtype = cls.guess_data_type(data)
91			if palette is None:
92			palette = cls.get_palette(None, dtype)
93			if dtype is DataType.qualitative:
94			if not isinstance(palette, ListedColormap):
95			raise TypeError(f"{palette} is not a valid choice for {dtype}")
96			if len(unique) > len(palette.colors):
97			raise ValueError(
98			f"Palette (N={len(palette.colors)}) too small for {len(unique)} items"
99			)
100			return {i: j for i, j in CommonTools.zip_strict(unique, map(to_hex, palette.colors))}
			0 ignored issues – show Unused Code introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Unnecessary use of a comprehension Loading history...
101			return palette
102
103			@classmethod
104			def get_palette(cls, name: Optional[str], data_type: Union[DataType, str]) -> Colormap:
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
105			data_type = DataType.of(data_type)
106			if name is None:
107			name = VIZ_RESOURCES.default_palettes[data_type.name]
108			if name in VIZ_RESOURCES.named_cmaps:
109			return VIZ_RESOURCES.named_cmaps[name]
110			return sns.color_palette(name, as_cmap=True)
111
112			@classmethod
113			def guess_data_type(cls, data: Sequence[Union[str, float]]) -> DataType:
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
114			numerical = cls._to_numerical(data)
115			if numerical is None:
116			return DataType.qualitative
117			is_divergent = cls._are_floats_divergent(data)
118			if is_divergent:
119			return DataType.divergent
120			return DataType.sequential
121
122			@classmethod
123			def _to_colors(cls, data: Sequence[Union[float, str]]) -> Optional[Sequence[str]]:
124			if not all((isinstance(d, str)) for d in data):
125			return None
126			try:
127			return [to_hex(c) for c in data]
128			except ValueError:
129			return None
130
131			@classmethod
132			def _to_numerical(cls, data: Sequence[Union[str, float]]) -> Optional[Sequence[float]]:
			0 ignored issues – show Unused Code introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Either all return statements in a function should return an expression, or none of them should. Loading history...
133			try:
134			[float(d) for d in data]
135			except ValueError:
136			return None
137
138			@classmethod
139			def _are_floats_divergent(cls, data: Sequence[float]):
140			signs = {np.sign(d) for d in data if d != 0 and not np.isnan(d) and not np.isinf(d)}
141			return len(signs) == 2
142
143			@classmethod
144			def context(
145			cls, style: Union[None, str, Path], kwargs: Optional[Mapping[str, Any]]
			0 ignored issues – show Coding Style introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
146			) -> Generator[None, None, None]:
147			"""
148			Override these from the default style.
149			This will be called once, at startup.
150			"""
151			new_kwargs = dict(VIZ_RESOURCES.override_settings["allow_change"])
152			if kwargs is not None:
153			new_kwargs.update(kwargs)
154			with plt.rc_context(new_kwargs, style):
155			yield
156
157			@classmethod
158			def fig_width_and_height(cls, size: str) -> Tuple[float, float]:
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
159			if size is None:
160			return plt.rcParams["figure.figsize"]
161			axis_to_str = {
162			i: d.strip() for i, d in enumerate(size.replace(" × ", " by ").split(" by "))
163			}
164			try:
165			default_inch = plt.rcParams["figure.figsize"]
166			width = cls._to_inch(axis_to_str.get(0), VIZ_RESOURCES.dims["widths"], default_inch[0])
167			height = cls._to_inch(
168			axis_to_str.get(1), VIZ_RESOURCES.dims["heights"], default_inch[1]
169			)
170			except ValueError:
171			raise ValueError(f"Strange --size format in '{size}'")
172			return width, height
173
174			@classmethod
175			def _to_inch(
			0 ignored issues – show Coding Style Naming introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Argument name "s" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
176			cls, s: Optional[str], standards: Mapping[str, float], default_inch: float
			0 ignored issues – show Coding Style introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
177			) -> float:
178			if s is None or len(s) == "":
179			return default_inch
180			try:
181			return float(s)
182			except ValueError:
183			pass
184			x = standards.get(s, s)
			0 ignored issues – show Coding Style Naming introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Variable name "x" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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...
185			return MiscUtils.canonicalize_quantity(x, "[length]").to("inch").magnitude
186
187
188			class MandosPlotUtils:
			0 ignored issues – show introduced 2021-09-09 01:56 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
189			@classmethod
190			def save(cls, figure: Figure, path: Path) -> None:
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
191			path.parent.mkdir(parents=True, exist_ok=True)
192			figure.savefig(str(path))
193			figure.clear()
194
195
196			CompoundStyleDf = (
197			TypedDfs.typed("CompoundStyleDf").require("inchikey", dtype=str).strict(cols=False).secure()
198			).build()
199
200			PredicateObjectStyleDf = (
201			TypedDfs.typed("PredicateObjectStyleDf")
202			.require("predicate", "object", dtype=str)
203			.strict(cols=False)
204			.secure()
205			).build()
206
207			PhiPsiStyleDf = (
208			TypedDfs.typed("PhiPsiStyleDf").require("phi", "psi", dtype=str).strict(cols=False).secure()
209			).build()
210
211
212			__all__ = [
213			"sns",
214			"plt",
215			"Figure",
216			"Axes",
217			"MandosPlotStyling",
218			"MandosPlotUtils",
219			"CompoundStyleDf",
220			"PredicateObjectStyleDf",
221			"VIZ_RESOURCES",
222			]
223

dmyersturnbull / mandos

Push — main ( 37036d...9cce85 )

VizResources._get_named_cmaps() A

Complexity

Size

Duplication

Importance

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