html_url,issue_url,id,node_id,user,created_at,updated_at,author_association,body,reactions,performed_via_github_app,issue
https://github.com/pydata/xarray/issues/2535#issuecomment-499919008,https://api.github.com/repos/pydata/xarray/issues/2535,499919008,MDEyOklzc3VlQ29tbWVudDQ5OTkxOTAwOA==,9096348,2019-06-07T15:00:08Z,2019-06-07T15:00:08Z,NONE,"Well the error occurs while writing the file. So if the reason is, that the file is corrupt then necdf4 is corrupting it... right? The problem is rather, that it does not even finish writing the file. 

FYI: The error does not occur at the same file every time.

Have a good weekend!! ;)","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,376389539
https://github.com/pydata/xarray/issues/2535#issuecomment-499876672,https://api.github.com/repos/pydata/xarray/issues/2535,499876672,MDEyOklzc3VlQ29tbWVudDQ5OTg3NjY3Mg==,9096348,2019-06-07T13:04:33Z,2019-06-07T13:04:33Z,NONE,"Hi there, 

I just wanted to let you know, that I do get the same error, when working with the following script. It does not use xarray or rasterio. So those will most likely not be the problem.

```python
class Gif2NetCDF():
    def __init__(self, netcdf_name, netcdf_destfolder, gif_folder,
                 gif_filter_pattern=None, detailled_conversion=True):
        """"""

        Parameters
        ----------
        netcdf_name : str
            specifying the name of the netcdf file to write.

        netcdf_destfolder : str
            specifying the folder where the netcdf file is supposed to be created

        giffolder : str
            specifying the folder that contains the gif files, that are supposed to be written as an netcdf

        gif_filter_pattern : str
            specifying a re pattern to filter the all files in directory so you end up with the gif files you want.
            The here specified string will be passed to re.match which will be checked for each file in the provided giffolder


        Examples
        --------

        ## defining variables
        import netCDF4
        netcdf_name = ""2016-07.nc""
        netcdf_destfolder = ""./example/radar""
        giffolder = ""./example/radar/2016-07/""

        ## create Instance
        cdf = Gif2NetCDF(netcdf_name, netcdf_destfolder, giffolder,gif_filter_pattern)
        ## write all (filtered) gifs in folder to netcdf file
        cdf.writeCDF()
        """"""

        ## creating global vars

        self.netcdf_name = netcdf_name
        self.netcdf_destfolder = netcdf_destfolder
        self.giffolder = gif_folder
        self.refilterpattern = gif_filter_pattern
        self.detailled_conversion = detailled_conversion

        self.netcdfFP = os.path.join(netcdf_destfolder, netcdf_name)

        # preparing the coordinate vectors
        self._lat_range = np.arange(479500, -160500, step=-1000)  # north
        self._long_range = np.arange(255500, 965500, step=1000)  # east

        # preparing time origin
        self.time_origin = dt.datetime.strptime(""1970-01-01 00:00:00"", ""%Y-%m-%d %H:%M:%S"")
        
        self.raincodes = np.array([....]) # this array is quite large, so I left it out... Which unfortunately means the code does not run... If anybody needs it please let me know

        return

    def list_gifs(self):
        self._gifs = os.listdir(self.giffolder)
        return self._gifs

    def filter_gifs(self):
        self._gifs = [file for file in self._gifs if re.match(self.refilterpattern, file)]
        return self._gifs

    def addDimensions(self):

        # adds dimensions to empty netcdf file
        self.latD = self.netcdfFile.createDimension('lat', self._lat_range.shape[0])  # north-south
        self.lonD = self.netcdfFile.createDimension('lon', self._long_range.shape[0])  # east-west
        self.timeD = self.netcdfFile.createDimension('time', None)

        return

    def addVariables(self):

        ## creating variables
        self.latV = self.netcdfFile.createVariable(""chy"", np.float32, (""lat"",), complevel=9, zlib=True)  # north-south
        self.lonV = self.netcdfFile.createVariable(""chx"", np.float32, (""lon"",), complevel=9, zlib=True)  # east-west
        self.timeV = self.netcdfFile.createVariable(""time"", np.float64, (""time"",), complevel=9, zlib=True)

        self.rainV = self.netcdfFile.createVariable(""rain"", np.float32, (""time"", ""lat"", ""lon""), complevel=9, zlib=True,
                                                    fill_value=-100)

        ## adding units
        self.latV.units = ""meters""
        self.lonV.units = ""meters""

        self.timeV.units = ""seconds""
        self.timeV.calender = ""standard""

        self.rainV.units = ""millimeter/hour""

        ## adding longname
        self.latV.long_name = ""swiss northing CH1903""
        self.lonV.long_name = ""swiss easting CH1903""
        self.timeV.long_name = ""seconds since 1970-01-01 00:00:00""

        self.rainV.long_name = ""precipitation intensity forecast""

        return

    def addDescription(self):

        self.netcdfFile.description = """"""...""""""

        self.netcdfFile.history = """"""Created: {}"""""".format(dt.datetime.now().strftime(""%Y-%m-%d %H:%M""))
        self.netcdfFile.source = '...'
        return

    def _write_static_dims(self):
        self.latV[:] = self._lat_range
        self.lonV[:] = self._long_range
        return

    def _write_time(self, file, datetime=None):

        if datetime is None:
            datestr = re.findall(""\.([0-9]+)\.gif"", file)[0]
            date = dt.datetime.strptime(datestr, ""%Y%m%d%H%M"")
        else:
            date = datetime

        seconds = (date - self.time_origin).total_seconds()
        current_size = self.timeV.size
        self.timeV[current_size] = seconds
        
        return

    def gif2array(self, file):
    
        xpix = 0
        ypix = 76
        n_pixel_x = 710 + xpix
        n_pixel_y = 640 + ypix

        gif = np.array(Image.open(file))[ypix:n_pixel_y, xpix:n_pixel_x].astype(""float64"")
        for idx, raincode in enumerate(self.raincodes):
            gif[gif == idx] = raincode[3]
        return gif

    def _write_rain(self, file):
        array = self.gif2array(os.path.join(self.giffolder, file))
        idx = self.rainV.shape[0] - 1
        self.rainV[idx, :, :] = array
        return

    def writeCDF(self):
        self.netcdfFile = Dataset(self.netcdfFP, 'w', format='NETCDF4_CLASSIC', )
        try:
            giflist = self.list_gifs()
            if self.refilterpattern is not None:
                fgiflist = self.filter_gifs()

            self.addDimensions()
            self.addVariables()
            self.addDescription()
            self._write_static_dims()

            for file in tqdm(self._gifs):
                self._write_time(file)
                self._write_rain(file)
                
        except Exception:
            self.netcdfFile.close()
            raise

        self.netcdfFile.close()

        return

```

**Error**

```python
Traceback (most recent call last):
.
.
.
  File ""C:\Users\foerstch\AppData\Local\Programs\Python\Python37\lib\site-packages\archiving\radar.py"", line 358, in _write_rain
    idx = self.rainV.shape[0] - 1
  File ""netCDF4\_netCDF4.pyx"", line 4031, in netCDF4._netCDF4.Variable.shape.__get__
  File ""netCDF4\_netCDF4.pyx"", line 3369, in netCDF4._netCDF4.Dimension.__len__
  File ""netCDF4\_netCDF4.pyx"", line 1857, in netCDF4._netCDF4._ensure_nc_success
RuntimeError: NetCDF: HDF error
```

Does anybody have some advice on how to fix this?

Thanks a bunch!
Christian","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,376389539