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annotate curve_fitting.py @ 0:8bf2c507af3a draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
author imgteam
date Thu, 22 Jul 2021 19:34:36 +0000
parents
children e0af18405e37
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0
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
imgteam
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1 """
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
imgteam
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2 Copyright 2021 Biomedical Computer Vision Group, Heidelberg University.
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
imgteam
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3 Author: Qi Gao (qi.gao@bioquant.uni-heidelberg.de)
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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4
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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5 Distributed under the MIT license.
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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6 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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7
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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8 """
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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9
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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10 import argparse
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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11
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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12 import numpy as np
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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13 import pandas as pd
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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14 from scipy.optimize import least_squares
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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17 def compute_curve(x, par):
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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18 assert len(par) in [2, 3], 'The degree of curve must be 1 or 2!'
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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19 if len(par) == 3:
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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20 return par[0] * x + par[1] + par[2] * x ** 2
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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21 elif len(par) == 2:
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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22 return par[0] * x + par[1]
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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25 def fitting_err(par, xx, seq, penalty):
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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26 assert penalty in ['abs', 'quadratic', 'student-t'], 'Unknown penalty function!'
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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27 curve = compute_curve(xx, par)
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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28 if penalty == 'abs':
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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29 err = np.sqrt(np.abs(curve - seq))
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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30 elif penalty == 'quadratic':
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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31 err = (curve - seq)
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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32 elif penalty == 'student-t':
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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33 a = 1000
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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34 b = 0.001
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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35 err = np.sqrt(a * np.log(1 + (b * (curve - seq)) ** 2))
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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36 return err
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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38
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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39 def curve_fitting(seq, degree=2, penalty='abs'):
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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40 assert len(seq) > 5, 'Data is too short for curve fitting!'
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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41 assert degree in [1, 2], 'The degree of curve must be 1 or 2!'
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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42
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43 par0 = [(seq[-1] - seq[0]) / len(seq), np.mean(seq[0:3])]
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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44 if degree == 2:
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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45 par0.append(-0.001)
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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46
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47 xx = np.array([i for i in range(len(seq))]) + 1
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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48 x = np.array(par0, dtype='float64')
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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49 result = least_squares(fitting_err, x, args=(xx, seq, penalty))
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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50
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51 return compute_curve(xx, result.x)
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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52
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53
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54 def curve_fitting_io(fn_in, fn_out, degree=2, penalty='abs', alpha=0.01):
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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55 # read all sheets
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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56 xl = pd.ExcelFile(fn_in)
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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57 nSpots = len(xl.sheet_names)
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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58 data_all = []
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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59 for i in range(nSpots):
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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60 df = pd.read_excel(xl, xl.sheet_names[i])
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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61 data_all.append(np.array(df))
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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62 col_names = df.columns.tolist()
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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63 ncols_ori = len(col_names)
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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64
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65 # curve_fitting
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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66 diff = np.array([], dtype=('float64'))
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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67 for i in range(nSpots):
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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68 seq = data_all[i][:, -1]
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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69 seq_fit = seq.copy()
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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70 idx_valid = ~np.isnan(seq)
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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71 seq_fit[idx_valid] = curve_fitting(seq[idx_valid], degree=2, penalty='abs')
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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72 data_all[i] = np.concatenate((data_all[i], seq_fit.reshape(-1, 1)), axis=1)
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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73 if alpha > 0:
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74 diff = np.concatenate((diff, seq_fit[idx_valid] - seq[idx_valid]))
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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75
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76 # add assistive curve
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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77 if alpha > 0:
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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78 sorted_diff = np.sort(diff)
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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79 fac = 1 - alpha / 2
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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80 sig3 = sorted_diff[int(diff.size * fac)]
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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81 for i in range(nSpots):
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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82 seq_assist = data_all[i][:, -1] + sig3
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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83 data_all[i] = np.concatenate((data_all[i], seq_assist.reshape(-1, 1)), axis=1)
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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84
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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85 # write to file
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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86 with pd.ExcelWriter(fn_out) as writer:
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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87 for i in range(nSpots):
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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88 df = pd.DataFrame()
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89 for c in range(ncols_ori):
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90 df[col_names[c]] = data_all[i][:, c]
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91 df['CURVE'] = data_all[i][:, ncols_ori]
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92 if alpha > 0:
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93 df['CURVE_A'] = data_all[i][:, ncols_ori + 1]
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94 df.to_excel(writer, sheet_name=xl.sheet_names[i], index=False, float_format='%.2f')
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95 writer.save()
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96
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97
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98 if __name__ == "__main__":
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99 parser = argparse.ArgumentParser(description="Fit (1st- or 2nd-degree) polynomial curves to data points")
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100 parser.add_argument("fn_in", help="File name of input data points (xlsx)")
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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101 parser.add_argument("fn_out", help="File name of output fitted curves (xlsx)")
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102 parser.add_argument("degree", type=int, help="Degree of the polynomial function")
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103 parser.add_argument("penalty", help="Optimization objective for fitting")
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104 parser.add_argument("alpha", type=float, help="Significance level for generating assistive curves")
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105 args = parser.parse_args()
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106 curve_fitting_io(args.fn_in, args.fn_out, args.degree, args.penalty, args.alpha)