Keras + pydot 中 Graphviz报错 真正原因与解决方法
Keras 报错 - OSError: pydot failed to call GraphViz.Please install GraphViz || pydot 报错 - FileNotFoundError: [WinError 2] “dot” not found in path. 的解决方法与真正原因
环境：windows、Anaconda、pydot 1.4.1
问题
出现以下两种情况的其中一种：
- keras 中调用 plot_model 函数报错：OSError:
pydotfailed to call GraphViz.Please install GraphViz (https://www.graphviz.org/) and ensure that its executables are in the $PATH. - pydot 报错：FileNotFoundError: [WinError 2] “dot” not found in path.
解决方法
一、首先确保 Graphviz 已正确安装，并已将其安装路径下的 bin 目录添加到环境变量。
二、使用：
import pydot
pydot?
Type: module
String form:
File: d:\anaconda3\lib\site-packages\pydot.py
Docstring: An interface to GraphViz.
找到 pydot.py 路径。
三、更改 pydot.py ，有两种更改方式，选择一种即可：
- 将 def get_executable_extension() 函数里的
return '.bat' if is_anacoda() else '.exe'改成return '.bat' if not is_anacoda() else '.exe'。如下：
def get_executable_extension():
# type: () -> str
if is_windows():
#return '.bat' if is_anacoda() else '.exe'
#ccg modify
return '.bat' if not is_anacoda() else '.exe'
else:
return ''
- 将 class Dot 里 init 函数的 self.prog 从 dot 改成 dot.exe，如下：
class Dot(Graph):
def __init__(self, *argsl, **argsd):
#self.prog = 'dot'
#ccg modify
self.prog = 'dot.exe'
原因分析
如此例中所示：
from keras.models import Sequential
from keras.layers import Input, Dense
from keras.utils.vis_utils import plot_model
model = Sequential()
model.add(Dense(50, input_shape=(100,)))
model.add(Dense(10))
plot_model(model, show_shapes=True)
在 Keras 中调用 plot_model 会报以下错误信息：（OSError: pydot failed to call GraphViz.Please install GraphViz (https://www.graphviz.org/) and ensure that its executables are in the $PATH.）
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
D:\Anaconda3\lib\site-packages\pydot.py in create(self, prog, format, encoding)
1917 arguments=arguments,
-> 1918 working_dir=tmp_dir,
1919 )
D:\Anaconda3\lib\site-packages\pydot.py in call_graphviz(program, arguments, working_dir, **kwargs)
138 stdout=subprocess.PIPE,
--> 139 **kwargs
140 )
D:\Anaconda3\lib\subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors)
728 errread, errwrite,
--> 729 restore_signals, start_new_session)
730 except:
D:\Anaconda3\lib\subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, unused_restore_signals, unused_start_new_session)
1016 os.fspath(cwd) if cwd is not None else None,
-> 1017 startupinfo)
1018 finally:
FileNotFoundError: [WinError 2] 系统找不到指定的文件。
During handling of the above exception, another exception occurred:
FileNotFoundError Traceback (most recent call last)
e:\mygit\projects\keras\keras\utils\vis_utils.py in _check_pydot()
25 # to check the pydot/graphviz installation.
---> 26 pydot.Dot.create(pydot.Dot())
27 except OSError:
D:\Anaconda3\lib\site-packages\pydot.py in create(self, prog, format, encoding)
1924 prog=prog)
-> 1925 raise OSError(*args)
1926 else:
FileNotFoundError: [WinError 2] "dot" not found in path.
During handling of the above exception, another exception occurred:
OSError Traceback (most recent call last)
in
----> 1 plot_model(model, show_shapes=True)
e:\mygit\projects\keras\keras\utils\vis_utils.py in plot_model(model, to_file, show_shapes, show_layer_names, rankdir, expand_nested, dpi)
216 """
217 dot = model_to_dot(model, show_shapes, show_layer_names, rankdir,
--> 218 expand_nested, dpi)
219 _, extension = os.path.splitext(to_file)
220 if not extension:
e:\mygit\projects\keras\keras\utils\vis_utils.py in model_to_dot(model, show_shapes, show_layer_names, rankdir, expand_nested, dpi, subgraph)
62 from ..models import Sequential
63
---> 64 _check_pydot()
65 if subgraph:
66 dot = pydot.Cluster(style='dashed', graph_name=model.name)
e:\mygit\projects\keras\keras\utils\vis_utils.py in _check_pydot()
27 except OSError:
28 raise OSError(
---> 29 '`pydot` failed to call GraphViz.'
30 'Please install GraphViz (https://www.graphviz.org/) '
31 'and ensure that its executables are in the $PATH.')
OSError: `pydot` failed to call GraphViz.Please install GraphViz (https://www.graphviz.org/) and ensure that its executables are in the $PATH.
通过错误信息加上分析源码发现徐错误流如下：
–> vis_utils.py plot_model()
–> vis_utils.py model_to_dot()
–> vis_utils.py _check_pydot()
–> vis_utils.py pydot.Dot.create(pydot.Dot())
测试：
import pydot
pydot.Dot.create(pydot.Dot())
会得到以下报错：（FileNotFoundError: [WinError 2] “dot” not found in path.）
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
D:\Anaconda3\lib\site-packages\pydot.py in create(self, prog, format, encoding)
1919 arguments=arguments,
-> 1920 working_dir=tmp_dir,
1921 )
D:\Anaconda3\lib\site-packages\pydot.py in call_graphviz(program, arguments, working_dir, **kwargs)
138 stdout=subprocess.PIPE,
--> 139 **kwargs
140 )
D:\Anaconda3\lib\subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors)
728 errread, errwrite,
--> 729 restore_signals, start_new_session)
730 except:
D:\Anaconda3\lib\subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, unused_restore_signals, unused_start_new_session)
1016 os.fspath(cwd) if cwd is not None else None,
-> 1017 startupinfo)
1018 finally:
FileNotFoundError: [WinError 2] 系统找不到指定的文件。
During handling of the above exception, another exception occurred:
FileNotFoundError Traceback (most recent call last)
in
----> 1 pydot.Dot.create(pydot.Dot())
D:\Anaconda3\lib\site-packages\pydot.py in create(self, prog, format, encoding)
1925 args[1] = '"{prog}" not found in path.'.format(
1926 prog=prog)
-> 1927 raise OSError(*args)
1928 else:
1929 raise
FileNotFoundError: [WinError 2] "dot" not found in path.
–> pydot.py Dot.create() 错误的原因即在此处，在 create 函数中调用 call_graphviz 时抛出了异常。可见 call_graphviz 的 program 参数传入的是 prog = self.prog = ‘dot’。
class Dot(Graph):
def __init__(self, *argsl, **argsd):
......
self.prog = 'dot'
......
def create(self, prog=None, format='ps', encoding=None):
if prog is None:
prog = self.prog
......
try:
stdout_data, stderr_data, process = call_graphviz(
program=prog,
arguments=arguments,
working_dir=tmp_dir,
)
except OSError as e:
if e.errno == errno.ENOENT:
args = list(e.args)
args[1] = '"{prog}" not found in path.'.format(
prog=prog)
raise OSError(*args)
else:
raise
......
return stdout_data
而 call_graphviz 函数对 program 参数的处理是 program += get_executable_extension()，即给 ‘dot’ 加上后缀名，照理说应该是 ‘.exe’。
def call_graphviz(program, arguments, working_dir, **kwargs):
if program in DEFAULT_PROGRAMS:
extension = get_executable_extension()
program += extension
......
env = {
'PATH': os.environ.get('PATH', ''),
'LD_LIBRARY_PATH': os.environ.get('LD_LIBRARY_PATH', ''),
}
......
return stdout_data, stderr_data, process
但是，get_executable_extension 得到的后缀名却并不是 ‘.exe’，代码如下，调用 get_executable_extension 得到的后缀名却是 ‘.bat’。pydot.py 中这部分的代码让人费解，这里正是问题的根源所在。
首先 is_windows()肯定是 True的，return的时候用了python的三目运算，当 is_anacoda()=Ture时返回 ‘.bat’，当 is_anacoda()=False时返回 ‘.exe’。
而安装了 Anaconda 环境 is_anacoda()判断的结果就是 True，所以返回的后缀名就是 ‘.bat’。而 Graphviz 安装 bin 目录下的程序是 dot.exe，并没有 dot.bat ，所以此时就程序就找不到了，从而报错。
def is_windows():
# type: () -> bool
return os.name == 'nt'
def is_anacoda():
# type: () -> bool
return os.path.exists(os.path.join(sys.prefix, 'conda-meta'))
def get_executable_extension():
# type: () -> str
if is_windows():
return '.bat' if is_anacoda() else '.exe'
else:
return ''
不知道 pydot 代码为什么这么写，但是知道原因就可以对症下药了，解决方法中的方式1即是在 is_anacoda()前加了个 not使程序后缀名返回 .exe。
而方式2是在class Dot 中 self.prog 从 ‘dot’ 改成了 ‘dot.exe’，这样传入 call_graphviz 的参数 program 就是 ‘dot.exe’，并且此时无法通过if program in DEFAULT_PROGRAMS的判断，也就不会再进行后面的 program+=get_executable_extension()了，此时程序也能找到 dot.exe 了。
终于可以愉快地使用 pydot 了，上面的简单模型画出来如下：
