Laboratoire RDP » Biophysics Team » FLORIVAR

#!/usr/bin/env python

# before lounching the executable activate the timagetk conda environement

# conda activate florivar

# general imports :

from sys import argv

import pandas as pd

import os

def read_areas(dirname):

    listfiles=os.listdir(dirname)

    listfiles=[i for i in listfiles if '-area.csv' in i]

    sepalname=[]

    area=[]

    for i in listfiles:

        name=i.split('-area.csv')[0]

        sepalname.append(name)

        df=pd.read_csv(dirname+i, delimiter=',')[:-2]

        A=sum(df['Value'])/2.

        area.append(A)

    data = {'Sepal': sepalname, 'Area': area}

    newdf=pd.DataFrame.from_dict(data)    

    newdf=newdf.sort_values("Sepal", ascending=True, inplace=False)

    return newdf

def read_measurements(fname):

    df=pd.read_csv(fname, delimiter=';')

    print("Reading file : ",fname)

    print("Number of entries at reading: ",df.shape)

    df['Sepal']=[name.split('_oriented')[0] for name in df['Sepal']]

    df=df.sort_values("Sepal", ascending=True, inplace=False)

    return df

measures_filename = argv[1]

areadir = argv[2]+'/'

root=measures_filename.split('.csv')[0]

outputfile=root+"_full.csv"

df=read_measurements(measures_filename)

newdf=read_areas(areadir)

#

df = pd.merge(df, newdf, left_on="Sepal", right_on="Sepal")

#

df['CurvedSF']=df['CurvedWidth']/df['CurvedLength']

df['FlatSF']=df['FlatWidth']/df['FlatLength']

#

df['Thickness']=df['volume']/df['Area']

#

df['GaussK']=1./df['LR']/df['TR']

df['CentralGaussK']=1./df['LR423']/df['TR423']

df.to_csv(outputfile, index=False, sep=";")

print("Number of entries : ",df.shape)

labels=list(df.columns[1:])

print('Columns written:',list(df.columns))

print('Sepals:',list(df['Sepal']))

print('Measurements written in file:',outputfile)