def renameFcsFile(Fpath):
for file in [
file for file in os.listdir(Fpath)
if os.path.splitext(file)[1] == ".fcs"
]:
filename = Fpath + '/' + file
fcs = Fcs(filename)
Fcs.panel_rename()
if __name__ == '__main__':
###################################################
#### 1.Read FCS file and convert to CSV ####
###################################################
# Choose File Path
Fpath = filedialog.askdirectory()
os.makedirs(Fpath + "/WriteFcs/")
csv_path = Fpath + '/WriteFcs/'
for filename in [
filename for filename in os.listdir(Fpath)
if os.path.splitext(filename)[1] == ".fcs"
]:
file = Fpath + '/' + filename
fcs = Fcs(file)
pars = fcs.pars
new_filename = re.sub("-", "", filename)
new_filename = re.sub("^.+?_", "", new_filename)
# new_filename = re.sub("^.+?_", "", new_filename)
new_file = Fpath + "/WriteFcs/" + new_filename + '.csv'
fcs.write_to(new_file, pars, to='csv')
path = Fpath + "/WriteFcs"
all_df = pd.DataFrame()
for file in os.listdir(path):
df = pd.read_csv(path + '/' + file)
all_df = all_df.append(df)
print("File %s has finished." % file)
all_df.iloc[:, :-1].to_csv(path + '/' + path.split('/')[-2] + '.csv',
index=False)
from FCS import Fcs
from tkinter import filedialog
import os
import re
from tkinter import Tk
# 选择路径
root = Tk()
root.withdraw()
Fpath = filedialog.askdirectory()
# 读取panel表信息
panel_file = Fpath + "/panel.xlsx"
panel_tuple = Fcs.export_panel_tuple(panel_file)
print(panel_tuple)
for filename in [
filename for filename in os.listdir(Fpath)
if os.path.splitext(filename)[1] == ".fcs"
]:
file = Fpath + '/' + filename
fcs = Fcs(file)
pars = fcs.delete_channel(fcs.pars, 89, 115, 140, 115)
# pars = fcs.marker_rename(fcs.pars, *panel_tuple)
# stain_channel_index = fcs.get_stain_channels(pars)
#
# # 添加event_length, 191, 193, 194, 140
# add_channel = ["Event_length", "Ir191Di", "Ir193Di", "Pt194Di", "Ce140Di"]
# add_index = [i + 1 for i in range(0, len(pars)) if pars[i].par_short_name in add_channel]
# stain_channel_index.extend(add_index)
if __name__ == '__main__':
###################################################
#### 1.Read FCS file and convert to CSV ####
###################################################
# Choose File Path
Fpath = filedialog.askdirectory()
os.makedirs(Fpath+"/WriteFcs/")
os.makedirs(Fpath+"/Output/")
csv_path = Fpath + '/WriteFcs/'
output_path = Fpath + '/Output/'
# Read Panel Information
panel_file = Fpath + "/panel.xlsx"
panel_tuple = Fcs.export_panel_tuple(panel_file)
print(panel_tuple)
for filename in [filename for filename in os.listdir(Fpath) if os.path.splitext(filename)[1] == ".fcs"]:
file = Fpath + '/' + filename
fcs = Fcs(file)
pars = fcs.marker_rename(fcs.pars, *panel_tuple)
stain_channel_index = fcs.get_stain_channels(pars)
# Add event_length, 191, 193, 194, 140
add_channel = ["Event_length", "Ir191Di", "Ir193Di", "Pt194Di", "Ce140Di"]
add_index = [i + 1 for i in range(0, len(pars)) if pars[i].par_short_name in add_channel]
stain_channel_index.extend(add_index)
pars = [pars[i] for i in range(0, len(pars)) if i + 1 in stain_channel_index]
# Rename new file
new_filename = re.sub("-", "", filename)
from FCS import Fcs
from tkinter import filedialog
import pandas as pd
import os
import re
if __name__ == '__main__':
# 选择路径
Fpath = filedialog.askdirectory()
os.makedirs(Fpath + "/WriteFcs/")
# 读取panel表信息
panel_file = Fpath + "/panel.xlsx"
panel_tuple = Fcs.export_panel_tuple(panel_file)
print(panel_tuple)
for filename in [
filename for filename in os.listdir(Fpath)
if os.path.splitext(filename)[1] == ".fcs"
]:
file = Fpath + '/' + filename
fcs = Fcs(file)
# 重写marker-name
pars = fcs.marker_rename(fcs.pars, *panel_tuple)
# 导出指定通道写出
# export_channel_tuple = ("Event_length", 115, 140, 144, 145, 148, 149, 153, 155, 158, 160, 163, 165, 170, 174, 191,
# 193, 194, 197, 198)
# pars = fcs.export_channel(pars, *export_channel_tuple)
# print(len(export_channel_tuple), len(pars))
from FCS import Fcs
from FCS import StainFcs
from FCS import Write
from tkinter import filedialog
import random
import os
# 选择路径
Fpath = filedialog.askdirectory()
for file in [
file for file in os.listdir(Fpath)
if os.path.splitext(file)[1] == ".fcs"
]:
filename = Fpath + '/' + file
fcs = Fcs(filename)
# # 写到excel中
# fcs.fcs2excel()
# 染色通道
# stain_fcs = StainFcs(filename)
# stain_fcs.fcs2excel(folder_name="Stain_excel")
# # 写出到fcs中
# save_dir = fcs.file_dir + "/WriteFcs"
# # excel文件夹不存在时创建
# if not os.path.exists(save_dir):
# os.makedirs(save_dir)
# filename = save_dir + '/' + file
#