mutis.astro

Complexity

Total Complexity

132

Size/Duplication

Total Lines	1131
Duplicated Lines	11.23 %

Importance

Changes

0

10 Functions

Rating	Name	Duplication	Size	Complexity
F	KnotsIdAuto()	0	115	20
A	pol_angle_reshape()	0	20	4
A	get_output()	0	16	2
B	KnotsIdReadMod_from_diffmap()	0	60	5
A	KnotsIdReadCSV()	0	44	4
F	KnotsId2dGUI()	64	305	42
C	KnotsIdSaveMod()	0	84	11
F	KnotsIdGUI()	63	250	31
A	KnotsIdSaveCSV()	0	46	3
B	KnotsIdReadMod()	0	80	7

# Licensed under a 3-clause BSD style license - see LICENSE

Too many lines in module (1130/1000)

"""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"]

log = logging.getLogger(__name__)

# TODO: to be able to save previous labels in _mod.mod and be kepto after processing with diffmap

TODO and FIXME comments should generally be avoided.

#############################################################################
### Output compatible with IPython widgets and with plain python console: ###
#
# With this we can follow follow a commen scheme:
#
# def someGUIfunction():
#     out = get_output()
#     ... gui things...
#         out.clear_output()
#         out.append_stdout('some msg')
#     out.display_output()
#
class plain_printer:

Missing class docstring

Class name "plain_printer" doesn't conform to PascalCase naming style ('[^\\W\\da-z][^\\W_]+$' pattern)

    @staticmethod
    def append_stdout(msg):

Missing function or method docstring

        print(msg, end='')
    @staticmethod
    def clear_output():

Missing function or method docstring

        print('\n')
    @staticmethod
    def display_output():

Missing function or method docstring

        pass
        

Trailing whitespace

def get_output():

Missing function or method docstring

    try:
        get_ipython().__class__.__name__

The expression get_ipython().__class__.__name__ does not seem to have sideeffects and its result is not used.

Undefined variable 'get_ipython'

The variable get_ipython does not seem to be defined.

Trailing whitespace

        import ipywidgets

Import outside toplevel (ipywidgets)

Unable to import 'ipywidgets'

        class pretty_printer(ipywidgets.Output):

Missing class docstring

Class name "pretty_printer" doesn't conform to PascalCase naming style ('[^\\W\\da-z][^\\W_]+$' pattern)

            def __init__(self, *args, **kwargs):

Useless super delegation in method '__init__'

                super().__init__(*args, **kwargs)
            def display_output(self):

Missing function or method docstring

                display(self)

Undefined variable 'display'

The variable display does not seem to be defined.

Trailing whitespace

        out = pretty_printer(layout={'border': '1px solid black'})
        

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        return out
    except:

General except handlers without types should be used sparingly.

        return plain_printer
#############################################################################
   

Trailing whitespace

Trailing whitespace

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):

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)

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

    """
       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)'.
       

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        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

    """
    

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

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    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)):

The variable date seems to be unused.

Too many nested blocks (6/5)

        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)):

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)

Exactly one space required after comma

                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 after bracket

No space allowed before bracket

                    for m in range(len(dist)):

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)

Consider using enumerate instead of iterating with range and len

                        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)')

Use lazy % formatting in logging functions

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

                    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

    log.debug('Finito!')
    

Trailing whitespace

    return mod




############################################
############## Knots 2D GUI ################
############################################

def KnotsId2dGUI(mod, twidth=0.75, use_arrows=False, arrow_pos=1.0):

This function exceeds the maximum number of variables (35/15).

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)

    """
        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

Unable to import 'matplotlib.widgets'

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

Trailing whitespace

    out = get_output()

    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-twidth < 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)

            if len(x) > 0:
                if label == '' or label == 'None': # if it is unlabelled, do not connect it.

Consider merging these comparisons with "in" to "label in ('', 'None')"

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

This line is too long as per the coding-style (110/100).

                else:
                    lineas.append(ax.plot(x, y, '.-', linewidth=0.6, alpha=0.4, label=label)[0])
            else:
                lineas.append(None)

            if use_arrows:
                if len(x) > 1 and label != '' and label != 'None':
                    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, 

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Wrong continued indentation (add 14 spaces).

                               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 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.

        for i, label in enumerate(knots_names):
            years = knots_jyears[label]
            idx = (val-twidth < 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)

            if lineas[i] is not None:

This code seems to be duplicated in your project.

                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:
                    if label == '' or label == 'None': # if it is unlabelled, do not connect it.

Consider merging these comparisons with "in" to "label in ('', 'None')"

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

This line is too long as per the coding-style (111/100).

                    else:
                        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[-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
                if len(x) > 1 and label != '' and label != 'None':
                    flechas[i] = ax.quiver(x[:-1], 

Trailing whitespace

                                       y[:-1], 

Trailing whitespace

Wrong continued indentation (add 4 spaces).

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

Trailing whitespace

Wrong continued indentation (add 4 spaces).

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

Wrong continued indentation (add 4 spaces).

Trailing whitespace

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

Wrong continued indentation (add 4 spaces).

Trailing whitespace

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

Trailing whitespace

Wrong continued indentation (add 4 spaces).

                                       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_names does not seem to be defined.

The variable knots_Y does not seem to be defined.

The variable knots_jyears 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_X 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().strip(' ')

            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)

            log.debug(f"Updated index {selected_ind} to {text.upper()}")

Use lazy % formatting in logging functions

        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_knot does not seem to be defined.

The variable selected_x does not seem to be defined.

The variable selected_y does not seem to be defined.

Exactly one space required after comma

The variable selected_ind 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-twidth < 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 

Trailing whitespace

No space allowed after bracket

            if np.sum(rect_idx) > 0:

This code seems to be duplicated in your project.

Unnecessary "else" after "break"

                textbox.set_val(label)
                

Trailing whitespace

                selected_knot = label
                selected_x = x[rect_idx].ravel()
                selected_y = y[rect_idx].ravel()
                selected_ind = knots[label].index[rect_idx]
                

Trailing whitespace

                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

Trailing whitespace

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

        # print epoch of selected points:
        if selected_knot is not None:
            out.clear_output()
            out.append_stdout('Selected:\n')
            for idx in selected_ind:
                #print(f"Selected {mod.loc[idx, 'label']} {mod.loc[idx, 'date']}")
                out.append_stdout(f" -> {mod.loc[idx, 'label']} {mod.loc[idx, 'date'].strftime('%Y-%m-%d')}\n")

This line is too long as per the coding-style (111/100).

Trailing whitespace

        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('')
        if event.key in ['E', 'e']:
            out.append_stdout('-> Close\n')
            plt.close()


    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

Import outside toplevel (mpl_toolkits.axes_grid1.make_axes_locatable)

Unable to import 'mpl_toolkits.axes_grid1'

    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, E to exit')

    print('Usage:',
          '-> S to select, R to rename, Q to deactivate selector, E to exit',
          '-> To delete the knot, name it with a whitespace', 

Trailing whitespace

          '-> You can select points from one component at a time',
          '-> If you use the zoom or movement tools, remember to unselect them',
          sep='\n')
        

Trailing whitespace

    plt.show()
    

Trailing whitespace

    out.display_output()
  

Trailing whitespace

    return mod




############################################
################ Knots GUI #################
############################################



def KnotsIdGUI(mod):

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)

This function exceeds the maximum number of variables (28/15).

    """
        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

Unable to import 'matplotlib.widgets'

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

Trailing whitespace

    out = get_output()

    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 "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 len(x) > 0:
                if label == '' or label == 'None': # if it is unlabelled, do not connect it.

Consider merging these comparisons with "in" to "label in ('', 'None')"

                    lineas.append(ax.plot(x, y, '.', linewidth=0.8, alpha=0.5, label=label, color='black')[0])

This line is too long as per the coding-style (110/100).

                else:
                    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 "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 lineas[i] is not None:

This code seems to be duplicated in your project.

                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:
                    if label == '' or label == 'None': # if it is unlabelled, do not connect it.

Consider merging these comparisons with "in" to "label in ('', 'None')"

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

This line is too long as per the coding-style (111/100).

                    else:
                        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_values does not seem to be defined.

The variable knots_names 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.

        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().strip(' ')

            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 (20/15).

        nonlocal selected_knot,selected_date, selected_flux, selected_ind

The variable selected_ind does not seem to be defined.

Exactly one space required after comma

The variable selected_knot does not seem to be defined.

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 "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_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) 

No space allowed after bracket

Trailing whitespace

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}')

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

Use lazy % formatting in logging functions

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

        # print epoch of selected points:
        if selected_knot is not None:
            out.clear_output()
            out.append_stdout('Selected:\n')
            for idx in selected_ind:
                #print(f"Selected {mod.loc[idx, 'label']} {mod.loc[idx, 'date']}")
                out.append_stdout(f" -> {mod.loc[idx, 'label']} {mod.loc[idx, 'date'].strftime('%Y-%m-%d')}\n")

This line is too long as per the coding-style (111/100).

Trailing whitespace

        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('')
        if event.key in ['E', 'e']:
            out.append_stdout('-> Close\n')
            plt.close()


    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

Unable to import 'mpl_toolkits.axes_grid1'

Import outside toplevel (mpl_toolkits.axes_grid1.make_axes_locatable)

    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])))
    

Trailing whitespace

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

    print('Usage:',
          '-> S to select, R to rename, Q to deactivate selector, E to exit',
          '-> To delete the knot, name it with a whitespace', 

Trailing whitespace

          '-> You can select points from one component at a time',
          '-> If you use the zoom or movement tools, remember to unselect them',
          sep='\n')
        

Trailing whitespace

    plt.show()
    

Trailing whitespace

    out.display_output()

    return mod



###################################################
########### Knots Read Mod (diffmap only) #########
###################################################

def KnotsIdReadMod_from_diffmap(path=None):

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

    """
        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

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

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']))

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

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

    # 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)))

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

Trailing whitespace

    return mod


###################################################
################## Knots Save Mod #################
###################################################

def KnotsIdSaveMod(mod, path=None, rewrite=False, drop_blanks=False):

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)

    """
        Save Knots data to *_mod.mod files ready to be re-proccessed with diffmap.
        

Trailing whitespace

        Actually only useful to remove stupid knots and fit it again with diffmap.
        

Trailing whitespace

        Parameters:
        -----------
         mod : :pd.DataFrame:
             pandas.DataFrame containing every knot
         path: :str:
             string containing the path to which the files are to be saved, eg:
             path = 'my_knots/'
         rewrite: :bool:
             If rewrite is True, path is interpreted as a regex for which files
             to overwrite.
         drop_blanks: :bool:
             If True, knots without label (or whose label is a whitspace) are dropped.
             If False (default), they are saved without label.
             

Trailing whitespace

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

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

Trailing whitespace

Trailing whitespace

    mod = mod.copy()


    if drop_blanks:
        mod = mod.drop(mod[mod['label'].str.strip('') == ''].index)
    

Trailing whitespace

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

Trailing whitespace

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    if rewrite:
        file_list = 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)
            

Trailing whitespace

            if not len(match) > 0:
                continue
            

Trailing whitespace

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

Trailing whitespace

            if date not in mod_dict:
                raise Exception('Specified regex includes files for which there are no knots')
                

Trailing whitespace

            file_list.append(f)

        if len(file_list) != len(mod_dict):
            raise Exception(f'Specified files by path regex does not match the number of epochs ({len(file_list)} vs {len(mod_dict)})')

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

    else:
        file_list = list()
        for date in mod_dict.keys():
               file_list.append(f"{path}/{date.strftime('%Y-%m-%d')}_mod.mod")

The indentation here looks off. 12 spaces were expected, but 15 were found.

Trailing whitespace

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    for fname, (date, data) in zip(file_list, mod_dict.items()):
        data = data.copy()
        

Trailing whitespace

        #data = data.drop(columns=['label'])
        #data = data.drop(columns=['X'])
        #data = data.drop(columns=['Y'])
        

Trailing whitespace

        data['Flux (Jy)'] = data['Flux (Jy)'].astype(str) + 'v'
        data['Radius (mas)'] = data['Radius (mas)'].astype(str) + 'v'
        data['Theta (deg)'] = data['Theta (deg)'].astype(str) + 'v'

        ## add previous labels in comments (so diffmap does not get stuck with it)
        data['label'] = '!' + data['label']

        with open(fname, 'w') as f:

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)

            f.write("! Generated by mutis\n"
                    "! Columns\n"
                    "! 'Flux (Jy)', 'Radius (mas)', 'Theta (deg)', 'Major FWHM (mas)', 'Axial ratio', 'Phi (deg)', 'T', 'Freq (Hz)', 'SpecIndex', '!label'\n")

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            data.to_csv(f,
                        columns=['Flux (Jy)', 'Radius (mas)', 'Theta (deg)', 'Major FWHM (mas)', 'Axial ratio', 'Phi (deg)', 'T', 'Freq (Hz)', 'SpecIndex', 'label'],

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                        index=False, sep=' ', header=None)

        

Trailing whitespace

###################################################
################## Knots Read Mod #################
###################################################        

Trailing whitespace

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def KnotsIdReadMod(path=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)

    """
        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.
        

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        It detects whether the file was generated by mutis. If it was then 

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        it searchs for a hidden label column to load previous label names (unnamed labels
   

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        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'.
             

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        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

    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)
        

Trailing whitespace

        with open(f) as fobj:
            firstline = fobj.readline()
            if firstline == '! Generated by mutis\n':

The if statement can be replaced with 'var = bool(test)'

                generated_by_mutis = True
            else:
                generated_by_mutis = False
                

Trailing whitespace

        if generated_by_mutis:
            data = pd.read_csv(f, sep='\s+', 

Trailing whitespace

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

                               skiprows=3, 

Trailing whitespace

                               #converters={'label':(lambda l: '' if l == '' else l)}, 

Trailing whitespace

                               dtype={'label':str},
                               names=['Flux (Jy)', 'Radius (mas)', 'Theta (deg)', 'Major FWHM (mas)', 'Axial ratio', 'Phi (deg)', 'T', 'Freq (Hz)', 'SpecIndex',

This line is too long as per the coding-style (160/100).

                                      'label'])
            data['label'] = data['label'].str.strip('!')
        else:
            data = 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'])

This line is too long as per the coding-style (188/100).

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

            #data.insert(0, 'label', value=None)
            data.insert(0, 'label', value='')

        data.insert(1, 'date', value=date)

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

        data.insert(5, 'X', data['Radius (mas)']*np.cos(np.pi/180*(data['Theta (deg)']-90)))
        data.insert(6, 'Y', data['Radius (mas)']*np.sin(np.pi/180*(data['Theta (deg)']-90)))

        mod_data.append(data)
             

Trailing whitespace

    # 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])
     

Trailing whitespace

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

Trailing whitespace

    return mod



###################################################
########### Knots CSV final outputting ############
###################################################

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)
        

Trailing whitespace

Trailing whitespace

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