<commit_before># -*- coding: utf-8 -*-
"""
    image.py

    General info
"""
from __future__ import division, unicode_literals, print_function

import math
from ..generic.signal import fit_to_type
from ..generic.rotation import find_rotation, apply_rotate_and_cleanup
from ..generic.registration import translation_2x1d
from .channel_detection import Channels
from ..debugging import DebugPlot
from ..generic.tunable import tunable


class BaseImage(object):
    """
        An image object stores the original image, rotation and cropping information as well as the modified image.
        It points to channel objects as well.
    """

    def __init__(self):
        self.image = None
        self.original_image = None

        # metadata

        self.multipoint = 0
        self.timepoint = 0.0
        self.timepoint_num = 0

        self.calibration_px_to_mu = 1.0  # uncalibrated

        # metadata

        self.metadata = {'x': 0.0,
                         'y': 0.0,
                         'z': 0.0,
                         'time': 0.0,
                         'timepoint': 0,
                         'multipoint': 0,
                         'calibration_px_to_mu': 1.0,
                         'tag': '',
                         'tag_number': 0}

        self.angle = float('NaN')
        self.crop_height = 0
        self.crop_width = 0

        self.shift = [0, 0]

    def setup_image(self, image):
        """

        :param image:
        """
        self.image = image
        self.original_image = image

    def pixel_to_mu(self, pix):
        """
        converts a distance in pixels to micrometers using the calibration data of the image

        :param pix: pixel distance to convert
        :return: distance in micrometers as floating point number
        """
        return float(self.calibration_px_to_mu * pix)

    def mu_to_pixel(self, mu):
        """
        converts a distance in micrometers to pixels using the calibration data of the image

        :param mu: micrometer distance to convert
        :return: distance in pixels as floating point number
        """
        return float(mu / self.calibration_px_to_mu)

    def cp(self, x, y):
        """
        calculate point. transforms one coordinate in rotated, cropped space to one in the original image

        :param x: x position
        :param y: y position
        :return: a tuple of floats
        """
        hw = (self.original_image.shape[1] - self.crop_width) / 2
        hh = (self.original_image.shape[0] - self.crop_height) / 2
        r = math.sqrt((x - hw) ** 2 + (y - hh) ** 2)
        phi = math.atan2(y - hh, x - hw)
        x = r * math.cos(phi + self.angle / (180.0 / math.pi)) + hw
        y = r * math.sin(phi + self.angle / (180.0 / math.pi)) + hh
        return [x + self.crop_width, y + self.crop_height]


class AutoRotationProvider(object):
    """
    This mixin class adds automatic rotation (by :py:func:`molyso.generic.rotation.find_rotation`) functionality to the Image class.
    """

    def __init__(self):
        super(AutoRotationProvider, self).__init__()
        self.angle = float('NaN')
        self.crop_height = 0.0
        self.crop_width = 0.0

    def autorotate(self):
        """
        performs automatic rotation detection, rotation and cropping of the image
        :returns: None
        """

        if self.angle != self.angle:
            self.angle = find_rotation(self.image, steps=
            tunable('orientation-detection.strips', 10, description="Number of strips for orientation correction."))

        # noinspection PyAttributeOutsideInit
        self.image, self.angle, self.crop_height, self.crop_width = \
            apply_rotate_and_cleanup(self.image, self.angle)


# noinspection PyUnresolvedReferences
class AutoRegistrationProvider(object):
    """
    This mixin class adds automatic registration (by :py:func:`molyso.generic.registration.translation_2x1d`) functionality to the Image class.
    """

    def __init__(self):
        super(AutoRegistrationProvider, self).__init__()
        self._fft_pair_cached = False
        self.shift = [0.0, 0.0]

    @property
    def fft_pair(self):
        """
        Retrieves the cached or calculates and caches the FT pair necessary for fast registration.

        :return:
        """
        if not getattr(self, '_fft_pair_cached', False):
            _, self._fft_pair_cached = translation_2x1d(self.original_image, self.original_image, return_a=True)
        return self._fft_pair_cached

    def autoregistration(self, reference):<commit_msg>safety assertion to fail early if rotation yields empty image<commit_after># -*- coding: utf-8 -*-
"""
    image.py

    General info
"""
from __future__ import division, unicode_literals, print_function

import math
from ..generic.signal import fit_to_type
from ..generic.rotation import find_rotation, apply_rotate_and_cleanup
from ..generic.registration import translation_2x1d
from .channel_detection import Channels
from ..debugging import DebugPlot
from ..generic.tunable import tunable


class BaseImage(object):
    """
        An image object stores the original image, rotation and cropping information as well as the modified image.
        It points to channel objects as well.
    """

    def __init__(self):
        self.image = None
        self.original_image = None

        # metadata

        self.multipoint = 0
        self.timepoint = 0.0
        self.timepoint_num = 0

        self.calibration_px_to_mu = 1.0  # uncalibrated

        # metadata

        self.metadata = {'x': 0.0,
                         'y': 0.0,
                         'z': 0.0,
                         'time': 0.0,
                         'timepoint': 0,
                         'multipoint': 0,
                         'calibration_px_to_mu': 1.0,
                         'tag': '',
                         'tag_number': 0}

        self.angle = float('NaN')
        self.crop_height = 0
        self.crop_width = 0

        self.shift = [0, 0]

    def setup_image(self, image):
        """

        :param image:
        """
        self.image = image
        self.original_image = image

    def pixel_to_mu(self, pix):
        """
        converts a distance in pixels to micrometers using the calibration data of the image

        :param pix: pixel distance to convert
        :return: distance in micrometers as floating point number
        """
        return float(self.calibration_px_to_mu * pix)

    def mu_to_pixel(self, mu):
        """
        converts a distance in micrometers to pixels using the calibration data of the image

        :param mu: micrometer distance to convert
        :return: distance in pixels as floating point number
        """
        return float(mu / self.calibration_px_to_mu)

    def cp(self, x, y):
        """
        calculate point. transforms one coordinate in rotated, cropped space to one in the original image

        :param x: x position
        :param y: y position
        :return: a tuple of floats
        """
        hw = (self.original_image.shape[1] - self.crop_width) / 2
        hh = (self.original_image.shape[0] - self.crop_height) / 2
        r = math.sqrt((x - hw) ** 2 + (y - hh) ** 2)
        phi = math.atan2(y - hh, x - hw)
        x = r * math.cos(phi + self.angle / (180.0 / math.pi)) + hw
        y = r * math.sin(phi + self.angle / (180.0 / math.pi)) + hh
        return [x + self.crop_width, y + self.crop_height]


class AutoRotationProvider(object):
    """
    This mixin class adds automatic rotation (by :py:func:`molyso.generic.rotation.find_rotation`) functionality to the Image class.
    """

    def __init__(self):
        super(AutoRotationProvider, self).__init__()
        self.angle = float('NaN')
        self.crop_height = 0.0
        self.crop_width = 0.0

    def autorotate(self):
        """
        performs automatic rotation detection, rotation and cropping of the image
        :returns: None
        """

        if self.angle != self.angle:
            self.angle = find_rotation(self.image, steps=
            tunable('orientation-detection.strips', 10, description="Number of strips for orientation correction."))

        # noinspection PyAttributeOutsideInit
        self.image, self.angle, self.crop_height, self.crop_width = \
            apply_rotate_and_cleanup(self.image, self.angle)

        assert self.image.size > 0


# noinspection PyUnresolvedReferences
class AutoRegistrationProvider(object):
    """
    This mixin class adds automatic registration (by :py:func:`molyso.generic.registration.translation_2x1d`) functionality to the Image class.
    """

    def __init__(self):
        super(AutoRegistrationProvider, self).__init__()
        self._fft_pair_cached = False
        self.shift = [0.0, 0.0]

    @property
    def fft_pair(self):
        """
        Retrieves the cached or calculates and caches the FT pair necessary for fast registration.

        :return:
        """
        if not getattr(self, '_fft_pair_cached', False):
            _, self._fft_pair_cached = translation_2x1d(self.original_image, self.original_image, return_a=True)
        return self._fft_pair_cached

    def autoregistration(self, reference):
{'fraction_non_alphanumeric': 0.09642857142857143, 'fraction_numerical': 0.012012987012987014, 'mean_word_length': 2.142128527711663, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 4, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3992576', 'n_tokens_mistral': 2763, 'n_tokens_neox': 2586, 'n_words': 763}