how to open dx file in Python

[jiaming]

Would anyone tell me how to open a dx file in Python? I got stuck here. Thanks a bunch.

[shivkumar123]

There are some docs/howtos/wiki you can find easily, like : https://griddataformats.readthedocs....ts/OpenDX.html

[jiaming]

Would you please send the full link again?Thanks. :)

[buran]

https://griddataformats.readthedocs.io/
And the link in the other post is https://griddataformats.readthedocs.io/e...penDX.html

[jiaming]

That's great. Thanks a lot.
I did use "from gridData import Grid". but got error mesg saying: "No module named 'gridData'". What else should I do to import Grid? Thanks again.

[buran]

You need to install it first
https://github.com/MDAnalysis/GridDataFormats
From what I see it is available via pip from PyPI

[jiaming]

Sorry to bother you again. I got ParseError as following:
g = Grid("ray.dx")

---------------------------------------------------------------------------
DXParseError Traceback (most recent call last)
<ipython-input-2-0a1918c382cd> in <module>()
----> 1 g = Grid("ray.dx")

~/anaconda3/lib/python3.7/site-packages/gridData/core.py in __init__(self, grid, edges, origin, delta, metadata, interpolation_spline_order)
115
116 if type(grid) is str:
--> 117 self.load(grid)
118 elif not (grid is None or edges is None):
119 # set up from histogramdd-type data

~/anaconda3/lib/python3.7/site-packages/gridData/core.py in load(self, filename, file_format)
300 """
301 loader = self._get_loader(filename, file_format=file_format)
--> 302 loader(filename)
303
304 def _load_python(self, filename):

~/anaconda3/lib/python3.7/site-packages/gridData/core.py in _load_dx(self, filename)
319 """Initializes Grid from a OpenDX file."""
320 dx = OpenDX.field(0)
--> 321 dx.read(filename)
322 grid, edges = dx.histogramdd()
323 self.__init__(grid=grid, edges=edges, metadata=self.metadata)

~/anaconda3/lib/python3.7/site-packages/gridData/OpenDX.py in read(self, file)
486 DXfield = self
487 p = DXParser(file)
--> 488 p.parse(DXfield)
489
490 def add(self,component,DXobj):

~/anaconda3/lib/python3.7/site-packages/gridData/OpenDX.py in parse(self, DXfield)
672 self.tokens = [] # token buffer
673 with open(self.filename,'r') as self.dxfile:
--> 674 self.use_parser('general') # parse the whole file and populate self.objects
675
676 # assemble field from objects

~/anaconda3/lib/python3.7/site-packages/gridData/OpenDX.py in use_parser(self, parsername)
930 """Set parsername as the current parser and apply it."""
931 self.__parser = self.parsers[parsername]
--> 932 self.__parser()
933 def set_parser(self,parsername):
934 """Set parsername as the current parser."""

~/anaconda3/lib/python3.7/site-packages/gridData/OpenDX.py in __general(self)
721 raise DXParseError('Unknown level-1 construct at '+str(tok))
722
--> 723 self.apply_parser() # hand over to new parser
724 # (possibly been set further down the hierarchy!)
725

~/anaconda3/lib/python3.7/site-packages/gridData/OpenDX.py in apply_parser(self)
936 def apply_parser(self):
937 """Apply the current parser to the token stream."""
--> 938 self.__parser()
939
940 def __tokenize(self,string):

~/anaconda3/lib/python3.7/site-packages/gridData/OpenDX.py in __array(self)
895 value = self.__consume().value()
896 else:
--> 897 raise DXParseError('array: '+str(tok)+' not recognized.')
898
899 def __field(self):

DXParseError: array: <token BARESTRING,shape> not recognized.

[buran]

are you sure this is OpenDX file?

[jiaming]

aha, openDX can be installed using "sudo apt-get install dx". so simple. I found it somewhere.
Yes, it is openDX file. I think the format is different tho. Anyway, the window pops up.
Thanks, buran. Really appreciate your help. And shivkumar123 also.