Update ReadFileTXTOlympus+FileResults.ipynb

%% Cell type:code id: tags:

``` python

#!/usr/bin/env python3

# -*- coding: utf-8 -*-

"""

Created on Tue Mar  8 15:42:39 2022

@author: elie

"""

```

%% Output

    '\nCreated on Tue Mar  8 15:42:39 2022\n\n@author: elie\n'

%% Cell type:code id: tags:

``` python

import warnings

warnings.simplefilter(action='ignore', category=FutureWarning)

import os

import javabridge

import bioformats

import xml.etree.ElementTree as ET

import pandas as pd

import numpy as np

```

%% Cell type:code id: tags:

``` python

def listdirectory(path):

    fichier=[]

    for root, dirs, files in os.walk(path):

        for i in files:

            if ".vsi" in i:

                path,ext=os.path.splitext(i)

                if (os.path.isfile(os.path.join(root, path+".vsi"))):

                    fichier.append(os.path.join(root, i))

    return sorted(fichier)

def _init_logger():

    """This is so that Javabridge doesn't spill out a lot of DEBUG messages

    during runtime.

    From CellProfiler/python-bioformats.

    """

    rootLoggerName = javabridge.get_static_field("org/slf4j/Logger",

                                         "ROOT_LOGGER_NAME",

                                         "Ljava/lang/String;")

    rootLogger = javabridge.static_call("org/slf4j/LoggerFactory",

                                "getLogger",

                                "(Ljava/lang/String;)Lorg/slf4j/Logger;",

                                rootLoggerName)

    logLevel = javabridge.get_static_field("ch/qos/logback/classic/Level",

                                   "WARN",

                                   "Lch/qos/logback/classic/Level;")

    javabridge.call(rootLogger,

            "setLevel",

            "(Lch/qos/logback/classic/Level;)V",

            logLevel)

def get_metadata(filename):

    """Read the meta data and return the metadata object.

    """

    meta = bioformats.get_omexml_metadata(filename)

    #metadata = bioformats.omexml.OMEXML(meta)

    return meta

```

%% Cell type:markdown id: tags:

## Indicate YOUR PATHs

%% Cell type:code id: tags:

``` python

# Path for vsi files and txt files (extract from CellSens)

pathchemin="/media/elie/8To/REDPOL/SaolomeNov2023/exemple"

pathchemin="/mypath"

# Path for csv file results

pathResult="/media/elie/8To/REDPOL/SaolomeNov2023/exemple"

pathResult="/mypath"

```

%% Cell type:code id: tags:

``` python

javabridge.start_vm(class_path=bioformats.JARS,run_headless=False)

logger = _init_logger()

print("Images : ",len(listdirectory(pathchemin)))

listfile=listdirectory(pathchemin)

for fileVSI in listfile: #154

    numero=fileVSI.split("/")[-1].split(".")[0].replace("Process_","")

    chemin = os.path.dirname(fileVSI)

    print("Process number :"+str(numero))

    if os.path.isfile(pathResult+"/_"+numero+"_resultat.csv"):

        if os.path.isfile(chemin+"/Process_"+numero+".txt"):

            "Read metadata to read real time"

            metadata = get_metadata(fileVSI)

            mdroot = ET.fromstring(metadata)

            df = pd.DataFrame(columns=['Chiffre', 'entete', 'temps ms'])

            for child in mdroot[3]:

                if "Acquisition Value #" in child[0][0][0].text:

                    chiffre=int(child[0][0][0].text.split("#")[1])

                    df2 = pd.DataFrame([[chiffre,child[0][0][0].text,child[0][0][1].text]], columns=['Chiffre', 'entete', 'temps ms'] )

                    #df=df.concat(df2,axis=0, join='outer')

                    df = df.append(df2)

            sorted_df = df.sort_values(by='Chiffre')

            if float(sorted_df.iat[3,2])<200:

                sorted_df.reset_index(drop = True, inplace = True)

                sorted_df=sorted_df.iloc[::2] # impair

                sorted_df.reset_index(drop = True, inplace = True)

                sorted_df = sorted_df.tail(-1)

                sorted_df = sorted_df.head(-1)

            else:

                sorted_df.reset_index(drop = True, inplace = True)

                sorted_df=sorted_df.iloc[1::2] # pair

                sorted_df.reset_index(drop = True, inplace = True)

                sorted_df = sorted_df.head(-2)

            sorted_df['Frame']=np.arange(len(sorted_df))

            df = pd.read_csv (pathResult+"/_"+numero+"_resultat.csv",sep=";")

            df3=df.join(sorted_df.set_index('Frame'), on='Sequence')

            "Read file text create by Cellsens "

            fileRead=open(chemin+"/Process_"+numero+".txt","r",encoding='UTF-16')

            data=fileRead.readlines()

            index = data.index("[Marker]\n")

            df3["Mark"]=""

            del df3['Chiffre']

            del df3['entete']

            compteur=1

            for line in range(len(data)-1,index,-1):

                timeStamp=float(data[line].replace("[","").replace("]","").replace(",",".").replace(" ms","").split("=")[0])

                #print(timeStamp)

                for chf in range(len(df3)-1):

                    if (float(df3.iat[chf,12])==timeStamp):

                        #print(df3.iat[chf,0])

                        df3.iat[chf,13]="Mark "+str(compteur)

                        compteur+=1

                    elif (float(df3.iat[chf,12])<=timeStamp) and (timeStamp<float(df3.iat[chf+1,12])):

                        #print(df3.iat[chf+1,0])

                        df3.iat[chf+1,13]="Mark "+str(compteur)

                        compteur+=1

            df3.to_csv(pathResult+"/_"+numero+"_new_resultat.csv",index=False,sep=";")

            #print("Mark number : "+str(compteur))

```

%% Output

    Images :  1

    Process number :34