python - 从 Python 脚本运行 ImageJ 宏错误未找到

Question

背景

我使用Python2.7并按照www.scivision.dev上的说明安装了Imagej没有任何问题。从终端运行时，该应用程序运行良好。

我使用的Java版本是

parovelb@Latitude-E6510:~$ java -version
openjdk version "11.0.2" 2019-01-15
OpenJDK Runtime Environment (build 11.0.2+9-Ubuntu-3ubuntu118.04.3)
OpenJDK 64-Bit Server VM (build 11.0.2+9-Ubuntu-3ubuntu118.04.3, mixed mode, sharing)

OpenJDK的路径在我的~/.bashrc中设置

# java path
PATH=/usr/lib/jvm/java-11-openjdk-amd64/bin/java:$PATH
export PATH

问题

我在 Python2.7 中的脚本中运行 ImageJ 宏时遇到问题。该脚本使用 subprocess.Popen 调用 ImageJ 宏。该宏创建一个 CSV 文件并将结果写入其中。这是我的脚本:

#!/usr/bin/python2.7 python2.7
#!/bin/sh -i
# -*- coding: utf-8 -*-


"""
This program runs an ImageJ macro.
"""


import os
import csv
import sys
import subprocess
from subprocess import PIPE, STDOUT
from collections import defaultdict


def Connector_Check():
    cmd = ["imagej", "-macro", "luerlocktest.ijm"]
    process = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.STDOUT)
    (stdoutdata, stderrdata) = process.communicate()
    print 'stdoutdata', stdoutdata

    # read result in row 1, col 2
    with open(" ~/results.csv","rb") as res:
        resReader = csv.reader(res)
        resReader = list(resReader)
        val = resReader[1][2]
    print "Connector check value = ", val


if __name__ == "__main__":
    # execute connector check
    Connector_Check()

如果我从终端运行命令 imagej -macro luerlocktest.ijm，它工作正常，但运行我的脚本会出现错误:

stdoutdata -macro: 1: -macro: imagej: not found

Traceback (most recent call last):
  File "wrapper_imagej.py", line 34, in <module>
    Connector_Check()
  File "wrapper_imagej.py", line 25, in Connector_Check
    with open("/home/parovelb/Desktop/CV/Results.csv","rb") as res:
IOError: [Errno 2] No such file or directory: '/home/parovelb/Desktop/CV/Results.csv'

不幸的是，下面的这些问答并不能解决我的问题:

1. How to connect ImageJ to python?
2. Using ImageJ Jython in Standalone Python IDE
3. Docker image error: “/bin/sh: 1: python: not found”

关于为什么imagej:找不到有什么建议吗？

<强>1。更新

使用Shell=False给出错误:

Traceback (most recent call last):
  File "wrapper_imagej.py", line 34, in <module>
    Connector_Check()
  File "wrapper_imagej.py", line 20, in Connector_Check
    process = subprocess.Popen(cmd, shell=False, stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.STDOUT)
  File "/usr/lib/python2.7/subprocess.py", line 394, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

Answer 1

使用 subprocess 打开 shell 不会使其执行 .bashrc，因此它永远不会看到 $PATH 的修改版本。您可以尝试将 shell=False 参数添加到 Popen() 调用中。其他选项包括以其他方式将 imagej 添加到您的 PATH 中，或者使用程序本身的完整路径调用 imagej，根本不需要 $PATH 变量。

例如:

cmd = ["/usr/lib/jvm/java-11-openjdk-amd64/bin/java/imagej", "-macro", "luerlocktest.ijm"]