Errors when run example 'Cu_111_pole_figure.py'

[fangchizhou]

Dear developers Thanks for creating the package which is exactly what I need for my project. However, when I tried to run the example Cu_111_pole_figure.py, it shows errors below ( I'm using python 3.6 on Pycharm on Windows 10). Really appreciate it if you can give me some feedback.

Regards

E:\untitled\venv\Scripts\python.exe E:/untitled/test.py Traceback (most recent call last): File "E:/untitled/test.py", line 13, in micro = Microstructure(name='Cu_111') File "F:\pymicro\pymicro\crystal\microstructure.py", line 1452, in init overwrite_hdf5, autodelete, keywords) File "F:\pymicro\pymicro\core\samples.py", line 218, in init self._init_file_object(sample_name, sample_description, keywords) File "F:\pymicro\pymicro\core\samples.py", line 1712, in _init_file_object self.h5_dataset = tables.File(self.h5_file, mode='r+') File "C:\Users\fangc\AppData\Local\Programs\Python\Python36\lib\site-packages\tables\file.py", line 778, in init self._g_new(filename, mode, **params) File "tables\hdf5extension.pyx", line 492, in tables.hdf5extension.File._g_new tables.exceptions.HDF5ExtError: HDF5 error back trace

File "D:\pytables_hdf5\CMake-hdf5-1.10.5\hdf5-1.10.5\src\H5F.c", line 509, in H5Fopen unable to open file File "D:\pytables_hdf5\CMake-hdf5-1.10.5\hdf5-1.10.5\src\H5Fint.c", line 1652, in H5F_open unable to read superblock File "D:\pytables_hdf5\CMake-hdf5-1.10.5\hdf5-1.10.5\src\H5Fsuper.c", line 623, in H5F__super_read truncated file: eof = 96, sblock->base_addr = 0, stored_eof = 2048

End of HDF5 error back trace

Unable to open/create file 'Cu_111_data.h5' Exception ignored in: <object repr() failed> Traceback (most recent call last): File "F:\pymicro\pymicro\core\samples.py", line 230, in del self.sync() File "F:\pymicro\pymicro\core\samples.py", line 478, in sync self.add_attributes(dic=self.content_index, nodename='/Index') AttributeError: 'Microstructure' object has no attribute 'content_index'

[heprom]

Hi Fangchizhou, I see the problem, we have recently (version 0.5.0) modified significantly how the Microstructure class works (now based on hdf5 to support large 3D microstructures). As a results, some of the examples are broken, I will fix it, thank you for letting me know. Henry

[heprom]

Hi Fangchizhou, I corrected the problem,you can use the last published version on pypi (0.5.1) or the master branch from the repository. Please let me know if everything is working for you. Regards Henry

[fangchizhou]

Hi Henry

Thank you very much. Really appreciate your help.

Regards Chizhou

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From: Henry Proudhonmailto:notifications@github.com Sent: Monday, January 25, 2021 3:23 PM To: heprom/pymicromailto:pymicro@noreply.github.com Cc: fangchizhoumailto:fangchizhou@live.com; Authormailto:author@noreply.github.com Subject: Re: [heprom/pymicro] Errors when run example 'Cu_111_pole_figure.py' (#8)

Hi Fangchizhou, I corrected the problem,you can use the last published version on pypi (0.5.1) or the master branch from the repository. Please let me know if everything is working for you. Regards Henry

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