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，该应用程序运行正常。

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的路径是在我的~/.bashrc

中设置的

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

问题

我在Python2.7中无法从脚本运行ImageJ宏。该脚本使用subprocess.Popen调用ImageJ宏。宏会创建一个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，它可以正常工作，但运行脚本会给我错误：

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，以下这些常见问题解答无法解决我的问题：

关于为什么imagej: not found的任何建议？

1。更新

使用Shell=False会出现错误：

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并不会使其执行.bashrc，因此它将永远不会看到$PATH的修改版本。您可以尝试将shell=False参数添加到Popen()调用中。其他选项包括以另一种方式将imagej添加到您的PATH或使用程序本身的完整路径调用imagej，完全不需要$PATH变量。

例如：

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

Answer 2

我确实更改了cmd的格式，并将ImageJ的安装路径放置在$HOME/ImageJ/ImageJ中。另外，我确实使用了单个命令行而不是列表。

不正确：

cmd = ["imagej", "-macro", "luerlocktest.ijm"]

正确：

cmd = ["$HOME/ImageJ/ImageJ -macro luerlocktest.ijm"]

找不到从Python脚本错误运行ImageJ宏

2 个答案: