8.Nipype中的Error

编写一两段程序，要是不出现几个错误，简直都对不起程序猿/程序媛这个光荣的名号了。教程中给出了若干种可能，以我自身为例就遇到过其中的绝大多数。在计算过程中，尽管Nipype会给出一部分的错误信息，比如：

180514-09:15:24,87 workflow INFO:
     Workflow preprocWF settings: ['check', 'execution', 'logging', 'monitoring']
180514-09:15:24,92 workflow INFO:
     Running serially.
180514-09:15:24,93 workflow INFO:
     [Node] Setting-up "preprocWF.selectfiles" in "/home/neuro/nipype_tutorial/notebooks/working_dir/preprocWF/selectfiles".
180514-09:15:24,97 workflow INFO:
     [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-09:15:24,105 workflow WARNING:
     [Node] Error on "preprocWF.selectfiles" (/home/neuro/nipype_tutorial/notebooks/working_dir/preprocWF/selectfiles)
180514-09:15:24,108 workflow ERROR:
     Node selectfiles failed to run on host 7eb1beccba8f.
180514-09:15:24,111 workflow ERROR:
     Saving crash info to /home/neuro/nipype_tutorial/notebooks/crash-20180514-091524-neuro-selectfiles-648d7b9b-092e-479a-b79c-c04ce2ba5774.pklz
Traceback (most recent call last):
  File "/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 480, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 564, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 644, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 521, in run
    outputs = self.aggregate_outputs(runtime)
  File "/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 595, in aggregate_outputs
    predicted_outputs = self._list_outputs()
  File "/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/interfaces/io.py", line 1402, in _list_outputs
    raise IOError(msg)
OSError: No files were found matching func template: /data/ds000114/sub-11/ses-test/func/sub-11_ses-test_task-fingerfootlips_bold.nii.gz

180514-09:15:24,112 workflow INFO:
     ***********************************
180514-09:15:24,113 workflow ERROR:
     could not run node: preprocWF.selectfiles
180514-09:15:24,114 workflow INFO:
     crashfile: /home/neuro/nipype_tutorial/notebooks/crash-20180514-091524-neuro-selectfiles-648d7b9b-092e-479a-b79c-c04ce2ba5774.pklz
180514-09:15:24,114 workflow INFO:
     ***********************************
RuntimeError: Workflow did not execute cleanly. Check log for details

从直接输出的Error Info中我们可以看到，这是一个OSError，主要是没有文件能够匹配给出的模板。但是，这些信息有时候却不能满足我们的需要。有时我们仍想查看更为具体的Error信息，就可以在命令行中使用如下命令来读取crashfile：

nipypecli crash <crashfile.pklz>

执行之后就会看到：

File: /home/neuro/nipype_tutorial/notebooks/crash-20180514-091524-neuro-selectfiles-648d7b9b-092e-479a-b79c-c04ce2ba5774.pklz
Node: preprocWF.selectfiles
Working directory: /home/neuro/nipype_tutorial/notebooks/working_dir/preprocWF/selectfiles


Node inputs:

base_directory = /data/ds000114
force_lists = False
ignore_exception = False
raise_on_empty = True
sort_filelist = True
subject_id = sub-11



Traceback: 
Traceback (most recent call last):
  File "/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 480, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 564, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 644, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 521, in run
    outputs = self.aggregate_outputs(runtime)
  File "/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 595, in aggregate_outputs
    predicted_outputs = self._list_outputs()
  File "/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/interfaces/io.py", line 1402, in _list_outputs
    raise IOError(msg)
OSError: No files were found matching func template: /data/ds000114/sub-11/ses-test/func/sub-11_ses-test_task-fingerfootlips_bold.nii.gz

一些更为具体的描述信息，包括节点的输入等，便于我们查找问题。

此外，通过-r参数，还可以使得崩溃的节点重新运行。(注意，这个我没有试过，只是官方的教程提到了，在这里记录一下）

如果所使用的模块不存在或没有进行配置，就需要手工来安装并进行配置，对于最常用的SPM可以这样选择不同的版本：

from nipype.interfaces.matlab import MatlabCommand
MatlabCommand.set_default_paths('/usr/local/MATLAB/R2017a/toolbox/spm12')

9. Debug

由于Nipype采用的Pipeline的处理方式，节点内部的操作都是封闭的，因此要想进行调试还是很不容易的。官方给出了一些调试的基本建议，包括：

1. 从单个被试开始，按照Linear，MultiProc，SGE的顺序，逐步完善程序
2. 启用调试模式：

from nipype import config
config.enable_debug_mode()

下面这个命令我没搞清楚是啥意思，官方的说法是：as the first import of your nipype script. To enable debug logging use:

from nipype import logging
logging.update_logging(config)

可能要通过实践来检验效果了。

官方还给了一些其他的调试方法和建议，我个人感觉现在用不到，就不记录了，先暂且放下来，以后慢慢消化吧。

这可能是这个系列的最后一部了，最后这些东西比较杂乱，正常搭建Workflow的时候基本用不到，下一步我想搭建一个类似于Gretna的Workflow，有机会的话把这个Workflow封装一下，做一个小软件。