mutis.astro

Complexity

Total Complexity

86

Size/Duplication

Total Lines	819
Duplicated Lines	11.36 %

Importance

Changes

0

8 Functions

Rating	Name	Duplication	Size	Complexity
A	KnotsIdReadCSV()	0	44	4
F	KnotsId2dGUI()	47	265	26
F	KnotsIdAuto()	0	113	20
A	pol_angle_reshape()	0	20	4
A	KnotsIdSaveMod()	0	2	1
F	KnotsIdGUI()	46	219	24
A	KnotsIdSaveCSV()	0	46	3
A	KnotsIdReadMod()	0	56	4

# Licensed under a 3-clause BSD style license - see LICENSE
"""Utils specific to the field of astrophysics"""

import logging

import numpy as np

Unable to import 'numpy'

import pandas as pd

Unable to import 'pandas'

import matplotlib as mplt

Unable to import 'matplotlib'

Unused matplotlib imported as mplt

import matplotlib.pyplot as plt

Unable to import 'matplotlib.pyplot'

import glob

standard import "import glob" should be placed before "import numpy as np"

import re

standard import "import re" should be placed before "import numpy as np"

from datetime import datetime

standard import "from datetime import datetime" should be placed before "import numpy as np"

from astropy.time import Time

Unable to import 'astropy.time'

__all__ = ["Astro"]

Undefined variable name 'Astro' in __all__

log = logging.getLogger(__name__)


def pol_angle_reshape(s):

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)

    """
        Reshape a signal as a polarization angle: shifting by 180 degrees in a way it varies as smoothly as possible.

This line is too long as per the coding-style (117/100).

    """
    

Trailing whitespace

    s = np.array(s)
    s = np.mod(s,180) # s % 180

Exactly one space required after comma

    sn = np.empty(s.shape)

Variable name "sn" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

    for i in range(1,len(s)):

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        #if t[i]-t[i-1] < 35:
        d = 181

Variable name "d" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        n = 0

Variable name "n" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        for m in range(0,100):

Variable name "m" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

Exactly one space required after comma

            m2 = (-1)**(m+1)*np.floor((m+1)/2)

Variable name "m2" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

            if np.abs(s[i]+180*m2-sn[i-1]) < d:
                d = np.abs(s[i]+180*m2-sn[i-1])

Variable name "d" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

                n = m2

Variable name "n" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        sn[i] = s[i]+180*n
    return sn 

Trailing whitespace

#########################################
################# Knots #################
#########################################



def  KnotsIdAuto(mod):

This function exceeds the maximum number of variables (18/15).

Function name "KnotsIdAuto" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

    """
       Identify the knots appearing in several epochs giving them names, based on their position.
       

Trailing whitespace

        Parameters:
        -----------
         mod : :pd.DataFrame:
             pandas.DataFrame containing every knot, with 

Trailing whitespace

             at least columns 'label', 'date', 'X', 'Y', 'Flux (Jy)'.
       

Trailing whitespace

        Returns: mod
        --------
         mod : :pd.DataFrame:
             pandas.DataFrame containing every knot with their altered labels, with 

Trailing whitespace

             at least columns 'label', 'date', 'X', 'Y', 'Flux (Jy)'.
         

Trailing whitespace

    """
    

Trailing whitespace

    mod_date_dict = dict(list((mod.groupby('date'))))
    

Trailing whitespace

    mod_dates = list(Time(list(mod_date_dict.keys())).datetime)
    mod_dates_str = list(Time(list(mod_date_dict.keys())).strftime('%Y-%m-%d'))
    mod_data = list(mod_date_dict.values())
    

Trailing whitespace

    Bx = [[]]*len(mod_dates)

Variable name "Bx" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

    By = [[]]*len(mod_dates)

Variable name "By" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

    B = [[]]*len(mod_dates)

Variable name "B" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

    thresh = 0.03 #0.062

    news = 0

    for i, (date, data) in enumerate(zip(mod_dates, mod_data)):

Too many nested blocks (6/5)

The variable date seems to be unused.

        log.debug(f'Analysing epoch i {i:3d} ({mod_dates_str[i]})')

Use lazy % formatting in logging functions

        if not len(data.index) > 0:
            log.error(' -> Error, no components found')
            break

        log.debug(f' it has {len(data.index)} components')

Use lazy % formatting in logging functions

        Bx[i] = np.ravel(data['X'])
        By[i] = np.ravel(data['Y'])
        B[i] = np.full(len(data.index), fill_value=None)

        # if first epoch, just give them new names...:
        if i == 0:
            log.debug(' first epoch, giving names...')

            for n in range(0,len(mod_data[i].index)):

Exactly one space required after comma

Variable name "n" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

                if data['Flux (Jy)'].iloc[n] < 0.001:
                    log.debug('  skipping, too weak')
                    break
                if n == 0:
                    B[i][n] = 'A0'
                else:
                    news = news + 1
                    B[i][n] = f'B{news}'
            log.debug(f' -> FOUND: {B[i]}\n')

Use lazy % formatting in logging functions

            continue

        # if not first epoch...:

        for n in range(0,len(mod_data[i].index)):

Exactly one space required after comma

Variable name "n" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

            if data['Flux (Jy)'].iloc[n] < 0.001:
                    log.debug('  skipping, too weak')

The indentation here looks off. 16 spaces were expected, but 20 were found.

                    break

The indentation here looks off. 16 spaces were expected, but 20 were found.

            if n == 0:
                B[i][n] = 'A0'
            else:
                log.debug(f' -> id component {n}...')

Use lazy % formatting in logging functions

                close = None

                a = 0

Variable name "a" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

                while ( i - a >= 0 and a < 4 and close is None):

No space allowed after bracket

                    a = a + 1

Variable name "a" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

                    if not len(Bx[i-a])>0:

Exactly one space required around comparison

                        break

                    dist = ( (Bx[i-a]-Bx[i][n]) ** 2 + (By[i-a]-By[i][n]) ** 2 ) ** 0.5

No space allowed before bracket

No space allowed after bracket

                    for m in range(len(dist)):

Consider using enumerate instead of iterating with range and len

Variable name "m" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

                        if B[i-a][m] in B[i]:
                            dist[m] = np.inf

                    if np.amin(dist) < thresh*a**1.5:
                        close = np.argmin(dist)

                    if B[i-a][close] in B[i]:
                            close = None

The indentation here looks off. 24 spaces were expected, but 28 were found.

                if close is None:
                    news = news + 1
                    B[i][n] = f'B{news}'
                    log.debug(f'   component {n} is new, naming it {B[i][n]}')

Use lazy % formatting in logging functions

                else:
                    log.debug(f'   component {n} is close to {B[i-a][close]} of previous epoch ({a} epochs before)')

This line is too long as per the coding-style (116/100).

Use lazy % formatting in logging functions

                    B[i][n] = B[i-a][close]


        log.debug(f' -> FOUND: {B[i]}\n')

Use lazy % formatting in logging functions

Trailing whitespace

Trailing whitespace

    for i, (date, data) in enumerate(zip(mod_dates, mod_data)):
        data['label'] = B[i]
         

Trailing whitespace

    mod = pd.concat(mod_data, ignore_index=True)
            

Trailing whitespace

    return mod



def KnotsId2dGUI(mod, use_arrows=False, arrow_pos=1.0):

Function name "KnotsId2dGUI" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

This function exceeds the maximum number of variables (33/15).

    """
        Prompt a GUI to select identified knots and alter their label, reprenting their 2D
        spatial distribution in different times.
        

Trailing whitespace

        It can be used inside jupyter notebooks, using '%matplotlib widget' first.
        

Trailing whitespace

        Parameters:
        -----------
         mod : :pd.DataFrame:
             pandas.DataFrame containing every knot, with at least columns 

Trailing whitespace

             'label', 'date', 'X', 'Y', 'Flux (Jy)'.
        

Trailing whitespace

        Returns:
        --------
         mod : :pd.DataFrame:
             pandas.DataFrame containing every knot with their altered labels, with 

Trailing whitespace

             at least columns 'label', 'date', 'X', 'Y', 'Flux (Jy)'.
    """
    

Trailing whitespace

    mod = mod.copy()
    

Trailing whitespace

    knots = dict(tuple(mod.groupby('label')))
    knots_names = list(knots.keys())
    knots_values = list(knots.values())
    knots_jyears = {k:Time(knots[k]['date'].to_numpy()).jyear for k in knots}
    knots_X = {k:knots[k]['X'].to_numpy() for k in knots}

Variable name "knots_X" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

    knots_Y = {k:knots[k]['Y'].to_numpy() for k in knots}

Variable name "knots_Y" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

    from matplotlib.widgets import Slider, Button, TextBox, RectangleSelector

Unused Button imported from matplotlib.widgets

Import outside toplevel (matplotlib.widgets.Slider, matplotlib.widgets.Button, matplotlib.widgets.TextBox, matplotlib.widgets.RectangleSelector)

Unable to import 'matplotlib.widgets'

    fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(8,8))

Exactly one space required after comma

Variable name "ax" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

    lineas = list()
    flechas = list()
    textos = list()

    def draw_all(val=2008):
        nonlocal lineas, flechas, textos

The variable textos does not seem to be defined.

The variable flechas does not seem to be defined.

The variable lineas does not seem to be defined.

        # instead of clearing the whole axis, remove artists
        for linea in lineas:
            if linea is not None:
                linea.remove()
        for texto in textos:
            if texto is not None:
                texto.remove()
        for flecha in flechas:
            if flecha is not None:
                flecha.remove()
        ax.set_prop_cycle(None)
        

Trailing whitespace

        lineas = list()
        flechas = list()
        textos = list()

        xlim, ylim = ax.get_xlim(), ax.get_ylim()
        

Trailing whitespace

        #ax.clear() # either clear the whole axis or remove every artist separetly
            

Trailing whitespace

        for i, label in enumerate(knots_names):
            years = knots_jyears[label]
            idx = (val-1.5 < years) & (years < val)
            x = knots_X[label][idx]

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)

            y = knots_Y[label][idx]

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)

            lineas.append(ax.plot(x, y, '.-', linewidth=0.6, alpha=0.4, label=label)[0])

            if use_arrows:
                if len(x) > 1:
                    flechas.append(ax.quiver(x[:-1], 

Trailing whitespace

                               y[:-1], 

Wrong continued indentation (add 14 spaces).

Trailing whitespace

                               arrow_pos*(x[1:] - x[:-1]), 

Wrong continued indentation (add 14 spaces).

Trailing whitespace

                               arrow_pos*(y[1:] - y[:-1]), 

Wrong continued indentation (add 14 spaces).

Trailing whitespace

                               scale_units='xy', angles='xy', scale=1, 

Wrong continued indentation (add 14 spaces).

Trailing whitespace

                               width=0.0015, headwidth=10, headlength=10, headaxislength=6,

Wrong continued indentation (add 14 spaces).

                               alpha=0.5, color=lineas[i].get_color()))

Wrong continued indentation (add 14 spaces).

                else:
                    flechas.append(None)

            if len(x) > 0:
                #textos.append(ax.annotate(label, (x[0], y[0]), (-28,-10), textcoords='offset points', color=lineas[i].get_color(), fontsize=14))

This line is too long as per the coding-style (145/100).

                textos.append(ax.text(x[-1]+0.015, y[-1]+0.015, label, {'color':lineas[i].get_color(), 'fontsize':14}))

This line is too long as per the coding-style (119/100).

            else:
                textos.append(None)

        ax.set_xlim(xlim)
        ax.set_ylim(ylim)
        ax.set_aspect('equal')
        

Trailing whitespace

        fig.canvas.draw_idle() # if removed every artist separately instead of ax.clear()

    draw_all()

    def update(val):
        nonlocal lineas, flechas, textos

The variable flechas does not seem to be defined.

The variable textos does not seem to be defined.

        for i, label in enumerate(knots_names):
            years = knots_jyears[label]
            idx = (val-1.5 < years) & (years < val)
            x = knots_X[label][idx]

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)

            y = knots_Y[label][idx]

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)

            lineas[i].set_xdata(x)
            lineas[i].set_ydata(y)

            if textos[i] is not None:
                if len(x) > 0:    

Trailing whitespace

                    textos[i].set_position((x[-1]+0.015, y[-1]+0.015))
                    textos[i].set_text(label)
                else:
                    textos[i].remove()
                    textos[i] = None
                    #textos[i].set_position((10, 10))
            else:
                if len(x) > 0:    

Trailing whitespace

                    textos[i] = ax.text(x[-1]+0.02, y[-1]+0.02, label, {'color':lineas[i].get_color(), 'fontsize':14})

This line is too long as per the coding-style (118/100).

            if use_arrows:
                if flechas[i] is not None:
                    flechas[i].remove()
                    flechas[i] = None

                flechas[i] = ax.quiver(x[:-1], 

Trailing whitespace

                                   y[:-1], 

Wrong continued indentation (add 4 spaces).

Trailing whitespace

                                   arrow_pos*(x[1:] - x[:-1]), 

Trailing whitespace

Wrong continued indentation (add 4 spaces).

                                   arrow_pos*(y[1:] - y[:-1]), 

Trailing whitespace

Wrong continued indentation (add 4 spaces).

                                   scale_units='xy', angles='xy', scale=1, 

Wrong continued indentation (add 4 spaces).

Trailing whitespace

                                   width=0.0015, headwidth=10, headlength=10, headaxislength=6, 

Wrong continued indentation (add 4 spaces).

Trailing whitespace

                                   alpha=0.5, color=lineas[i].get_color())

Wrong continued indentation (add 4 spaces).

        fig.canvas.draw_idle()



    selected_knot = None
    selected_ind = None
    selected_x = None
    selected_y = None


    def submit_textbox(text):

This code seems to be duplicated in your project.

        nonlocal mod, knots, knots_names, knots_values, knots_jyears, knots_X, knots_Y

The variable knots_values does not seem to be defined.

The variable knots_names does not seem to be defined.

The variable knots_Y does not seem to be defined.

The variable knots does not seem to be defined.

The variable knots_X does not seem to be defined.

The variable knots_jyears does not seem to be defined.

        log.debug('Submited with:')
        log.debug(f'   selected_knot {selected_knot}')

Use lazy % formatting in logging functions

        log.debug(f'   selected_ind {selected_ind}')

Use lazy % formatting in logging functions

        log.debug(f'   selected_x {selected_x}')

Use lazy % formatting in logging functions

        log.debug(f'   selected_y {selected_y}')

Use lazy % formatting in logging functions

        if selected_knot is not None:        

Trailing whitespace

            mod.loc[selected_ind, 'label'] = text.upper()

            knots = dict(tuple(mod.groupby('label')))
            knots_names = list(knots.keys())
            knots_values = list(knots.values())
            knots_jyears = {k:Time(knots[k]['date'].to_numpy()).jyear for k in knots}
            knots_X = {k:knots[k]['X'].to_numpy() for k in knots}

Variable name "knots_X" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

            knots_Y = {k:knots[k]['Y'].to_numpy() for k in knots}

Variable name "knots_Y" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

            print(f"Updated index {selected_ind} to {text.upper()}")
        else:
            pass

        draw_all(slider_date.val)

    def line_select_callback(eclick, erelease):

This function exceeds the maximum number of variables (17/15).

        nonlocal selected_knot,selected_x, selected_y, selected_ind

The variable selected_x does not seem to be defined.

The variable selected_knot does not seem to be defined.

The variable selected_ind does not seem to be defined.

Exactly one space required after comma

The variable selected_y does not seem to be defined.

        # 1 eclick and erelease are the press and release events
        x1, y1 = eclick.xdata, eclick.ydata

Variable name "x1" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

Variable name "y1" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        x2, y2 = erelease.xdata, erelease.ydata

Variable name "y2" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

Variable name "x2" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        log.debug("GUI: (%3.2f, %3.2f) --> (%3.2f, %3.2f)" % (x1, y1, x2, y2))

Use lazy % formatting in logging functions

        log.debug("GUI:  The button you used were: %s %s" % (eclick.button, erelease.button))

Use lazy % formatting in logging functions

        selected_knot = None
        selected_x = None
        selected_y = None
        selected_ind = None

        for i, label in enumerate(knots_names):

The variable i seems to be unused.

            years = knots_jyears[label]
            idx = (slider_date.val-1.5 < years) & (years < slider_date.val)

            if np.sum(idx) == 0:
                continue # we did not select any component from this component, next one

            x = np.array(knots_X[label])

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)

            y = np.array(knots_Y[label])

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)

            # get points iside current rectangle for current date
            rect_idx = (x1 < x) & ( x < x2) & (y1 < y) & ( y < y2) & idx 

No space allowed after bracket

Trailing whitespace

            if np.sum(rect_idx) > 0:

Unnecessary "else" after "break"

This code seems to be duplicated in your project.

                textbox.set_val(label)
                selected_knot = label
                selected_x = x[rect_idx].ravel()
                selected_y = y[rect_idx].ravel()
                selected_ind = knots[label].index[rect_idx]
                log.debug(f'Selected {label} points  rect_idx {rect_idx} x {x[rect_idx]}, y {y[rect_idx]} with indices {selected_ind}')

This line is too long as per the coding-style (135/100).

Use lazy % formatting in logging functions

                textbox.begin_typing(None)
                break # if we find selected components in this epoch, continue with renaming
            else:
                pass

        update(slider_date.val)


    def toggle_selector(event):

This code seems to be duplicated in your project.

        log.debug('GUI: Key pressed.')
        if event.key in ['Q', 'q'] and toggle_selector.RS.active:
            log.debug('Selector deactivated.')
            toggle_selector.RS.set_active(False)
        if event.key in ['S', 's'] and not toggle_selector.RS.active:
            log.debug('Selector activated.')
            toggle_selector.RS.set_active(True)
        if event.key in ['R', 'r']:
            log.debug('Selector deactivated.')
            toggle_selector.RS.set_active(False)
            textbox.begin_typing(None)
            #textbox.set_val('')


    toggle_selector.RS = RectangleSelector(ax, line_select_callback,
                                           drawtype='box', useblit=True,
                                           button=[1, 3],  # don't use middle button
                                           minspanx=0, minspany=0,
                                           spancoords='data',
                                           interactive=False)


    #plt.connect('key_press_event', toggle_selector)
    fig.canvas.mpl_connect('key_press_event', toggle_selector)



    from mpl_toolkits.axes_grid1 import make_axes_locatable

Unable to import 'mpl_toolkits.axes_grid1'

Import outside toplevel (mpl_toolkits.axes_grid1.make_axes_locatable)

    divider_slider = make_axes_locatable(ax)
    slider_ax = divider_slider.append_axes("top", size="3%", pad="4%")  

Trailing whitespace

    slider_date = Slider(ax=slider_ax, label="Date", valmin=2007, valmax=2020, valinit=2008, valstep=0.2, orientation="horizontal")

This line is too long as per the coding-style (131/100).

    slider_date.on_changed(update)

    #divider_textbox = make_axes_locatable(ax)
    #textbox_ax = divider_textbox.append_axes("bottom", size="3%", pad="4%") 

Trailing whitespace

    textbox_ax = fig.add_axes([0.3,0.015,0.5,0.05])

Exactly one space required after comma

    textbox = TextBox(textbox_ax, 'Knot name:', initial='None')
    textbox.on_submit(submit_textbox)



    ax.set_xlim([-1.0, +1.0])
    ax.set_ylim([-1.0, +1.0])
    ax.set_aspect('equal')

    fig.suptitle('S to select, R to rename, Q to deactivate selector')

    print('S to select, R to rename, Q to deactivate selector')
    print('(you can select points from one component at a time)')
    print('(if you use the zoom or movement tools, remember to unselect them)')

    plt.show()
    

Trailing whitespace

    return mod






def KnotsIdGUI(mod):

This function exceeds the maximum number of variables (27/15).

Function name "KnotsIdGUI" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

    """
        Prompt a GUI to select identified knots and alter their label, reprenting their
        time evolution.
        

Trailing whitespace

        It can be used inside jupyter notebooks, using '%matplotlib widget' first.
       

Trailing whitespace

        Parameters:
        -----------
         mod : :pd.DataFrame:
             pandas.DataFrame containing every knot, with at least columns 

Trailing whitespace

             'label', 'date', 'X', 'Y', 'Flux (Jy)'.
        

Trailing whitespace

        Returns:
        --------
         mod : :pd.DataFrame:
             pandas.DataFrame containing every knot with their altered labels, with 

Trailing whitespace

             at least columns 'label', 'date', 'X', 'Y', 'Flux (Jy)'.
    """
    

Trailing whitespace

    mod = mod.copy()
    

Trailing whitespace

    knots = dict(tuple(mod.groupby('label')))
    knots_names = list(knots.keys())
    knots_values = list(knots.values())
    knots_jyears = {k:Time(knots[k]['date'].to_numpy()).jyear for k in knots}
    knots_dates = {k:knots[k]['date'].to_numpy() for k in knots}
    knots_fluxes = {k:knots[k]['Flux (Jy)'].to_numpy() for k in knots}

    from matplotlib.widgets import TextBox, RectangleSelector

Import outside toplevel (matplotlib.widgets.TextBox, matplotlib.widgets.RectangleSelector)

Unable to import 'matplotlib.widgets'

    fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(8,5))

Variable name "ax" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

Exactly one space required after comma

Trailing whitespace

    lineas = list()
    textos = list()
    

Trailing whitespace

    def draw_all():
        nonlocal lineas, textos

The variable textos does not seem to be defined.

The variable lineas does not seem to be defined.

        for linea in lineas:
            if linea is not None:
                linea.remove()
        for texto in textos:
            if texto is not None:
                texto.remove()

        ax.set_prop_cycle(None)
        

Trailing whitespace

        lineas = list()
        textos = list()
        

Trailing whitespace

        #ax.clear() # either clear the whole axis or remove every artist separetly
        

Trailing whitespace

        for i, label in enumerate(knots_names):
            x, y = knots_jyears[label], knots_fluxes[label]

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)

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)

            if len(x) > 0:
                lineas.append(ax.plot(x, y, '.-', linewidth=0.8, alpha=0.5, label=label)[0])
            else:
                lineas.append(None)
                

Trailing whitespace

            if len(x) > 0:
                #textos.append(ax.annotate(label, (x[0], y[0]), (-28,-10), textcoords='offset points', color=lineas[i].get_color(), fontsize=14))

This line is too long as per the coding-style (145/100).

                textos.append(ax.text(x[0], y[0], label, {'color':lineas[i].get_color(), 'fontsize':14}))

This line is too long as per the coding-style (105/100).

            else:
                textos.append(None)
                

Trailing whitespace

        fig.canvas.draw_idle() # if removed every artist separately instead of ax.clear()


    def update():
        nonlocal lineas, textos

The variable textos does not seem to be defined.

The variable lineas does not seem to be defined.

        for i, label in enumerate(knots_names):   

Trailing whitespace

            x, y = knots_jyears[label], knots_fluxes[label]

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)

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)

            if lineas[i] is not None:
                if len(x) > 0:
                    lineas[i].set_xdata(x)
                    lineas[i].set_ydata(y)
                else:
                    lineas[i].remove()
                    lineas[i] = None
            else:
                if len(x) > 0:    

Trailing whitespace

                    lineas[i] = ax.plot(x, y, '.-', linewidth=0.8, alpha=0.5, label=label)[0]
        

Trailing whitespace

            if textos[i] is not None:
                if len(x) > 0:    

Trailing whitespace

                    textos[i].set_position((x[0], y[0]))
                    textos[i].set_text(label)
                else:
                    textos[i].remove()
                    textos[i] = None
                    #textos[i].set_position((10, 10))
            else:
                if len(x) > 0:    

Trailing whitespace

                    #textos[i] = ax.annotate(label, (x[0], y[0]), (-24,-10), textcoords='offset points', color=lineas[i].get_color(), fontsize=15)

This line is too long as per the coding-style (146/100).

                    textos[i] = ax.text(x[0], y[0], label, {'color':lineas[i].get_color(), 'fontsize':14})

This line is too long as per the coding-style (106/100).

Trailing whitespace

        fig.canvas.draw_idle()    

Trailing whitespace

Trailing whitespace

    selected_knot = None
    selected_ind = None
    selected_date = None
    selected_flux = None
    

Trailing whitespace

    def submit_textbox(text):

This code seems to be duplicated in your project.

        nonlocal mod, knots, knots_names, knots_values, knots_jyears, knots_dates, knots_fluxes

The variable knots_jyears does not seem to be defined.

The variable knots_dates does not seem to be defined.

The variable knots_fluxes does not seem to be defined.

The variable knots does not seem to be defined.

The variable knots_values does not seem to be defined.

The variable knots_names does not seem to be defined.

        log.debug('Submited with:')
        log.debug(f'   selected_knot {selected_knot}')

Use lazy % formatting in logging functions

        log.debug(f'   selected_ind {selected_ind}')

Use lazy % formatting in logging functions

        log.debug(f'   selected_flux {selected_flux}')

Use lazy % formatting in logging functions

        log.debug(f'   selected_date {selected_date}')

Use lazy % formatting in logging functions

        if selected_knot is not None:        

Trailing whitespace

            mod.loc[selected_ind, 'label'] = text.upper()

            knots = dict(tuple(mod.groupby('label')))
            knots_names = list(knots.keys())
            knots_values = list(knots.values())
            knots_jyears = {k:Time(knots[k]['date'].to_numpy()).jyear for k in knots}
            knots_dates = {k:knots[k]['date'].to_numpy() for k in knots}
            knots_fluxes = {k:knots[k]['Flux (Jy)'].to_numpy() for k in knots}

            print(f"Updated index {selected_ind} to {text.upper()}")
        else:
            pass
        

Trailing whitespace

        draw_all()

    def line_select_callback(eclick, erelease):

This function exceeds the maximum number of variables (19/15).

        nonlocal selected_knot,selected_date, selected_flux, selected_ind

The variable selected_ind does not seem to be defined.

The variable selected_knot does not seem to be defined.

Exactly one space required after comma

The variable selected_date does not seem to be defined.

The variable selected_flux does not seem to be defined.

        # 1 eclick and erelease are the press and release events
        x1, y1 = eclick.xdata, eclick.ydata

Variable name "y1" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

Variable name "x1" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        x2, y2 = erelease.xdata, erelease.ydata

Variable name "x2" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

Variable name "y2" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        log.debug("GUI: (%3.2f, %3.2f) --> (%3.2f, %3.2f)" % (x1, y1, x2, y2))

Use lazy % formatting in logging functions

        log.debug("GUI:  The button you used were: %s %s" % (eclick.button, erelease.button))

Use lazy % formatting in logging functions

        selected_knot = None
        selected_date = None
        selected_flux = None
        selected_ind = None

        for i, label in enumerate(knots_names):

The variable i seems to be unused.

            years = knots_jyears[label]
            fluxes = knots_fluxes[label]
            

Trailing whitespace

            # get points iside current rectangle for current date
            rect_idx = (x1 < years) & ( years < x2) & (y1 < fluxes) & ( fluxes < y2) 

Trailing whitespace

No space allowed after bracket

Trailing whitespace

            if np.sum(rect_idx) == 0:
                continue # we did not select any component from this component, next one

            x = np.array(years)

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)

            y = np.array(fluxes)

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)

            if np.sum(rect_idx) > 0:

Unnecessary "else" after "break"

This code seems to be duplicated in your project.

                textbox.set_val(label)
                selected_knot = label
                selected_x = x[rect_idx].ravel()

The variable selected_x seems to be unused.

                selected_y = y[rect_idx].ravel()

The variable selected_y seems to be unused.

                selected_ind = knots[label].index[rect_idx]
                log.debug(f'Selected {label} points  rect_idx {rect_idx} date {x[rect_idx]}, flux {y[rect_idx]} with indices {selected_ind}')

Use lazy % formatting in logging functions

This line is too long as per the coding-style (141/100).

                break # if we find selected components in this epoch, continue with renaming
            else:
                pass

        update()


    def toggle_selector(event):

This code seems to be duplicated in your project.

        log.debug('GUI: Key pressed.')
        if event.key in ['Q', 'q'] and toggle_selector.RS.active:
            log.debug('Selector deactivated.')
            toggle_selector.RS.set_active(False)
        if event.key in ['S', 's'] and not toggle_selector.RS.active:
            log.debug('Selector activated.')
            toggle_selector.RS.set_active(True)
        if event.key in ['R', 'r']:
            log.debug('Selector deactivated.')
            toggle_selector.RS.set_active(False)
            textbox.begin_typing(None)
            #textbox.set_val('')


    toggle_selector.RS = RectangleSelector(ax, line_select_callback,
                                           drawtype='box', useblit=True,
                                           button=[1, 3],  # don't use middle button
                                           minspanx=0, minspany=0,
                                           spancoords='data',
                                           interactive=False)


    fig.canvas.mpl_connect('key_press_event', toggle_selector)
    

Trailing whitespace

    from mpl_toolkits.axes_grid1 import make_axes_locatable

Import outside toplevel (mpl_toolkits.axes_grid1.make_axes_locatable)

Unable to import 'mpl_toolkits.axes_grid1'

    divider_textbox = make_axes_locatable(ax)
    textbox_ax = divider_textbox.append_axes("bottom", size="10%", pad="15%") 

Trailing whitespace

    #textbox_ax = fig.add_axes([0.3,0,0.5,0.05])
    textbox = TextBox(textbox_ax, 'Knot name:', initial='None')
    textbox.on_submit(submit_textbox)
    

Trailing whitespace

    draw_all()
    

Trailing whitespace

    #ax.autoscale()
    ax.set_xlabel('date (year)')
    ax.set_ylabel('Flux (Jy)')
    ax.set_title('Flux from each component')
    

Trailing whitespace

    xlims = Time(np.amin(mod['date'])).jyear, Time(np.amax(mod['date'])).jyear
    ax.set_xlim((xlims[0]-0.03*np.abs(xlims[1]-xlims[0]), xlims[1]+0.03*np.abs(xlims[1]-xlims[0])))
    plt.show()

    return mod



def KnotsIdReadMod(path=None, file_list=None):

Function name "KnotsIdReadMod" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

The argument file_list seems to be unused.

    """
        Read *_mod.mod files as printed by diffmap, return a dataframe containing all information ready

This line is too long as per the coding-style (103/100).

        to be worked on for labelling and to be used with these GUIs.
   

Trailing whitespace

        Parameters:
        -----------
         path : :str:
             string indicating the path to the mod files to be used, their names must end in the format

This line is too long as per the coding-style (103/100).

             '%Y-%m-%d_mod.mod', for example, path = 'vlbi/ftree/*/*_mod.mod'.
             

Trailing whitespace

        Returns:
        -----------
         mod : :pd.DataFrame:
             pandas.DataFrame containing every knot, with at least columns 

Trailing whitespace

             'label', 'date', 'X', 'Y', 'Flux (Jy)'.
    """
    

Trailing whitespace

    mod_dates_str = list()
    mod_dates = list()
    mod_data = list()

    for f in glob.glob(f'{path}'):

Variable name "f" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        match = re.findall(r'([0-9]{4}-[0-9]{2}-[0-9]{2})_mod.mod', f)
        if not len(match) > 0:
            continue

        date_str = match[0]
        date = datetime.strptime(date_str, '%Y-%m-%d')

        mod_dates_str.append(date_str)
        mod_dates.append(date)
        mod_data.append(pd.read_csv(f, sep='\s+', comment='!', names=['Flux (Jy)', 'Radius (mas)', 'Theta (deg)', 'Major FWHM (mas)', 'Axial ratio', 'Phi (deg)', 'T', 'Freq (Hz)', 'SpecIndex']))

A suspicious escape sequence \s was found. Did you maybe forget to add an r prefix?

This line is too long as per the coding-style (194/100).

    # sort by date    

Trailing whitespace

    idx = np.argsort(mod_dates)
    mod_dates_str = list(np.array(mod_dates_str, dtype=object)[idx])
    mod_dates = list(np.array(mod_dates, dtype=object)[idx])
    mod_data = list(np.array(mod_data, dtype=object)[idx])

    # fix stupid 'v' in columns, insert a label field, add X, Y columns
    for i in range(len(mod_dates)):

Consider using enumerate instead of iterating with range and len

        mod_data[i].insert(0, 'label', value=None)
        mod_data[i].insert(1, 'date', value=mod_dates[i])

        mod_data[i]['Flux (Jy)'] = mod_data[i]['Flux (Jy)'].str.strip('v').astype(float)
        mod_data[i]['Radius (mas)'] = mod_data[i]['Radius (mas)'].str.strip('v').astype(float)
        mod_data[i]['Theta (deg)'] = mod_data[i]['Theta (deg)'].str.strip('v').astype(float)

        mod_data[i].insert(5, 'X', mod_data[i]['Radius (mas)']*np.cos(np.pi/180*(mod_data[i]['Theta (deg)']-90)))

This line is too long as per the coding-style (113/100).

        mod_data[i].insert(6, 'Y', mod_data[i]['Radius (mas)']*np.sin(np.pi/180*(mod_data[i]['Theta (deg)']-90)))

This line is too long as per the coding-style (113/100).

Trailing whitespace

    mod = pd.concat(mod_data, ignore_index=True)
    

Trailing whitespace

    return mod


def KnotsIdSaveMod(mod, path=None):

The argument path seems to be unused.

Function name "KnotsIdSaveMod" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

The argument mod seems to be unused.

Missing function or method docstring

    pass

def KnotsIdReadCSV(path=None):

Function name "KnotsIdReadCSV" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

    """
        Read Knots data to .csv files (as done by Svetlana? ##)
        

Trailing whitespace

        Each knot label has its own {label}.csv. To be compatible with Svetlana's format, 

Trailing whitespace

        columns should be modified to:
        'Date' (jyear), 'MJD', 'X(mas)', 'Y(mas)', 'Flux(Jy)'
        These columns are derived from the ones in `mod`, old ones are removed.
        

Trailing whitespace

        Parameters:
        -----------
         path: :str:
             string containing the path to read files from eg:
             path = 'myknows/*.csv'
        Returns:
        --------
         mod : :pd.DataFrame:
             pandas.DataFrame containing every knot, with at least columns 

Trailing whitespace

             'label', 'date', 'X', 'Y', 'Flux (Jy)'.
    """
    

Trailing whitespace

    if path is None:
        log.error('Path not specified')
        raise Exception('Path not specified')
    

Trailing whitespace

    dataL = list()

Variable name "dataL" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

Trailing whitespace

    for f in glob.glob(f'{path}'):

Variable name "f" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        match = re.findall(r'/(.*).csv', f)
        

Trailing whitespace

        if not len(match) > 0:
            continue
        

Trailing whitespace

        knot_name = match[0]
        

Trailing whitespace

        log.debug(f'Loading {knot_name} from {f}')

Use lazy % formatting in logging functions

Trailing whitespace

        knot_data = pd.read_csv(f, parse_dates=['date'], date_parser=pd.to_datetime)
        

Trailing whitespace

        dataL.append((knot_name, knot_data))
    

Trailing whitespace

    mod = pd.concat(dict(dataL), ignore_index=True)

    return mod



def KnotsIdSaveCSV(mod, path=None):

Function name "KnotsIdSaveCSV" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

    """
        Save Knots data to .csv files (as done by Svetlana? ##)
        

Trailing whitespace

        Each knot label has its own {label}.csv. To be compatible with Svetlana's format, 

Trailing whitespace

        columns should be modified to:
        'Date' (jyear), 'MJD', 'X(mas)', 'Y(mas)', 'Flux(Jy)'
        These columns are derived from the ones in `mod`, old ones are removed.
        

Trailing whitespace

        Parameters:
        -----------
         mod : :pd.DataFrame:
             pandas.DataFrame containing every knot, with at least columns 

Trailing whitespace

             'label', 'date', 'X', 'Y', 'Flux (Jy)'.
         path: :str:
             string containing the path to which the files are to be saved, eg:
             path = 'my_knots/'
             

Trailing whitespace

        Returns:
        --------
         None
    """
    

Trailing whitespace

    if path is None:
        log.error('Path not specified')
        raise Exception('Path not specified')
        

Trailing whitespace

Trailing whitespace

    mod = mod.copy()
    

Trailing whitespace

Trailing whitespace

    mod_dict = dict(list(mod.groupby('label')))
    

Trailing whitespace

    for label, data in mod_dict.items():
        data = data.copy()
        

Trailing whitespace

        #data.insert(0, 'Date', Time(data['date']).jyear)
        #data.insert(1, 'MJD', Time(data['date']).mjd)
        #data = data.rename(columns={'X': 'X (mas)', 'Y': 'Y (mas)'})
        #data = data.drop(columns=['date'])
        #data = data.drop(columns=['label'])
        #if 'Radius (mas)' in data.columns:
        #    data = data.rename(columns={'Radius (mas)':'R(mas)'})
        #data.columns = data.columns.str.replace(' ', '')
        

Trailing whitespace

        data.to_csv(f'{path}/{label}.csv', index=False) 

Final newline missing