BLO output writer not working for lazy signals

[din14970]

It seems that the BLO writer does not work for lazy signals. The error seems to be in the line containing tofile. This is problematic for converting larger 4DSTEM/NBED datasets to BLO. I'll try to fix this.
In addition, the writer is very particular about units and does not seem to accept angstroms.

[hakonanes]

FYI, the writer was written by Vidar, @vidartf.

Yeah, I guess you have to write each pattern to memory in the loop

hyperspy/hyperspy/io_plugins/blockfile.py

Lines 290 to 293 in 2ddc359

	for img in signal._iterate_signal():
	dp_head.tofile(f)
	img.astype(endianess + 'u1').tofile(f)
	dp_head['ID'] += 1

[ericpre]

Can you please provide the traceback, in #2777, I can't see what changes would fix saving lazy signal.

[din14970]

The issue is that dask arrays don't have thtofile method that np has.

Full tracebacks for reference (on RELEASE_next_patch bd1c12b74):

When one does not run into unit conversion issues (e.g. set signal units to nm):

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-11-ebacc5399fa7> in <module>
----> 1 data_file.save("test.blo")

~/Documents/PythonProjects/FORKS/hyperspy/hyperspy/signal.py in save(self, filename, overwrite, extension, **kwds)
   2838         if extension is not None:
   2839             filename = filename.with_suffix(f".{extension}")
-> 2840         io.save(filename, self, overwrite=overwrite, **kwds)
   2841 
   2842     def _replot(self):

~/Documents/PythonProjects/FORKS/hyperspy/hyperspy/io.py in save(filename, signal, overwrite, **kwds)
    781         # Pass as a string for now, pathlib.Path not
    782         # properly supported in io_plugins
--> 783         writer.file_writer(str(filename), signal, **kwds)
    784 
    785         _logger.info(f'{filename} was created')

~/Documents/PythonProjects/FORKS/hyperspy/hyperspy/io_plugins/blockfile.py in file_writer(filename, signal, **kwds)
    274             endianess +
    275             'u1')
--> 276         vbf.tofile(f)
    277         # Zero pad until next data block
    278         if f.tell() > int(header['Data_offset_2']):

AttributeError: 'Array' object has no attribute 'tofile'

Dimension issue (signal unit is 1/nm):

---------------------------------------------------------------------------
DimensionalityError                       Traceback (most recent call last)
<ipython-input-9-ebacc5399fa7> in <module>
----> 1 data_file.save("test.blo")

~/Documents/PythonProjects/FORKS/hyperspy/hyperspy/signal.py in save(self, filename, overwrite, extension, **kwds)
   2838         if extension is not None:
   2839             filename = filename.with_suffix(f".{extension}")
-> 2840         io.save(filename, self, overwrite=overwrite, **kwds)
   2841 
   2842     def _replot(self):

~/Documents/PythonProjects/FORKS/hyperspy/hyperspy/io.py in save(filename, signal, overwrite, **kwds)
    781         # Pass as a string for now, pathlib.Path not
    782         # properly supported in io_plugins
--> 783         writer.file_writer(str(filename), signal, **kwds)
    784 
    785         _logger.info(f'{filename} was created')

~/Documents/PythonProjects/FORKS/hyperspy/hyperspy/io_plugins/blockfile.py in file_writer(filename, signal, **kwds)
    257 def file_writer(filename, signal, **kwds):
    258     endianess = kwds.pop('endianess', '<')
--> 259     header, note = get_header_from_signal(signal, endianess=endianess)
    260     with open(filename, 'wb') as f:
    261         # Write header

~/Documents/PythonProjects/FORKS/hyperspy/hyperspy/io_plugins/blockfile.py in get_header_from_signal(signal, endianess)
    111     axes_manager = signal.axes_manager.deepcopy()
    112     axes_manager.convert_units('navigation', 'nm')
--> 113     axes_manager.convert_units('signal', 'cm')
    114 
    115     if axes_manager.navigation_dimension == 2:

~/Documents/PythonProjects/FORKS/hyperspy/hyperspy/axes.py in convert_units(self, axes, units, same_units, factor)
   1131                 offset = self.navigation_dimension if convert_navigation else 0
   1132                 units_sig = units[offset:]
-> 1133                 self._convert_axes_to_same_units(self.signal_axes,
   1134                                                  units_sig, factor)
   1135         else:

~/Documents/PythonProjects/FORKS/hyperspy/hyperspy/axes.py in _convert_axes_to_same_units(self, axes, units, factor)
   1147         # Set the same units for all axes, use the unit of the first axis
   1148         # as reference
-> 1149         axes[0].convert_to_units(units[0], factor=factor)
   1150         unit = axes[0].units  # after conversion, in case units[0] was None.
   1151         for axis in axes[1:]:

~/Documents/PythonProjects/FORKS/hyperspy/hyperspy/axes.py in convert_to_units(self, units, inplace, factor)
    156             out = self._convert_compact_units(factor, inplace=inplace)
    157         else:
--> 158             out = self._convert_units(units, inplace=inplace)
    159         return out
    160 

~/Documents/PythonProjects/FORKS/hyperspy/hyperspy/axes.py in _convert_units(self, converted_units, inplace)
    125         scale_pint = self.scale * _ureg(self.units)
    126         offset_pint = self.offset * _ureg(self.units)
--> 127         scale = float(scale_pint.to(_ureg(converted_units)).magnitude)
    128         offset = float(offset_pint.to(_ureg(converted_units)).magnitude)
    129         units = '{:~}'.format(scale_pint.to(_ureg(converted_units)).units)

~/opt/anaconda3/envs/hyperspy-dev/lib/python3.8/site-packages/pint/quantity.py in to(self, other, *contexts, **ctx_kwargs)
    659         other = to_units_container(other, self._REGISTRY)
    660 
--> 661         magnitude = self._convert_magnitude_not_inplace(other, *contexts, **ctx_kwargs)
    662 
    663         return self.__class__(magnitude, other)

~/opt/anaconda3/envs/hyperspy-dev/lib/python3.8/site-packages/pint/quantity.py in _convert_magnitude_not_inplace(self, other, *contexts, **ctx_kwargs)
    608                 return self._REGISTRY.convert(self._magnitude, self._units, other)
    609 
--> 610         return self._REGISTRY.convert(self._magnitude, self._units, other)
    611 
    612     def _convert_magnitude(self, other, *contexts, **ctx_kwargs):

~/opt/anaconda3/envs/hyperspy-dev/lib/python3.8/site-packages/pint/registry.py in convert(self, value, src, dst, inplace)
    952             return value
    953 
--> 954         return self._convert(value, src, dst, inplace)
    955 
    956     def _convert(self, value, src, dst, inplace=False, check_dimensionality=True):

~/opt/anaconda3/envs/hyperspy-dev/lib/python3.8/site-packages/pint/registry.py in _convert(self, value, src, dst, inplace)
   1838                 value, src = src._magnitude, src._units
   1839 
-> 1840         return super()._convert(value, src, dst, inplace)
   1841 
   1842     def _get_compatible_units(self, input_units, group_or_system):

~/opt/anaconda3/envs/hyperspy-dev/lib/python3.8/site-packages/pint/registry.py in _convert(self, value, src, dst, inplace)
   1440 
   1441         if not (src_offset_unit or dst_offset_unit):
-> 1442             return super()._convert(value, src, dst, inplace)
   1443 
   1444         src_dim = self._get_dimensionality(src)

~/opt/anaconda3/envs/hyperspy-dev/lib/python3.8/site-packages/pint/registry.py in _convert(self, value, src, dst, inplace, check_dimensionality)
    985             # then the conversion cannot be performed.
    986             if src_dim != dst_dim:
--> 987                 raise DimensionalityError(src, dst, src_dim, dst_dim)
    988 
    989         # Here src and dst have only multiplicative units left. Thus we can

DimensionalityError: Cannot convert from '1 / nanometer' (1 / [length]) to 'centimeter' ([length])

It would seem that most 4D STEM datasets will run into this Dimension issue since DP's should have 1/length units. I guess real information about the geometry of the projector system / camera would be required and translated to the ASTAR coordinate system for a proper calibration.