Merge pull request #2908 from LMSC-NTappy/support_hamamatsu_streak

Support for Hamamatsu Streak tiff metadata

doc/user_guide/io.rst

@@ -772,17 +772,46 @@ Currently HyperSpy has limited support for reading and saving the TIFF tags.
 However, the way that HyperSpy reads and saves the scale and the units of TIFF
 files is compatible with ImageJ/Fiji and Gatan Digital Micrograph software.
 HyperSpy can also import the scale and the units from TIFF files saved using
-FEI, Zeiss SEM and Olympus SIS software.
+FEI, Zeiss SEM, Olympus SIS, Jeol SightX and Hamamatsu HPD-TA (streak camera)
+software.
+
+Extra loading arguments
+^^^^^^^^^^^^^^^^^^^^^^^
+
+- ``force_read_resolution`` (bool, optional): Force read image resolution using
+  the x_resolution, y_resolution and resolution_unit tags of the TIFF. Beware:
+  most software don't (properly) use these tags when saving TIFF files. Default
+  is ``False``.
+- ``hamamatsu_streak_axis_type`` (str, optional): decide the type of the
+  time axis for hamamatsu streak files:
+
+  * if ``uniform``, the best-fit linear axis is used, inducing a (small)
+    linearisation error. Initialise a UniformDataAxis.
+  * if ``data``, the raw time axis parsed from the metadata is used. Initialise
+    a DataAxis.
+  * if ``functional``, the best-fit 3rd-order polynomial axis is used, avoiding
+    linearisation error. Initialise a FunctionalDataAxis.
+
+By default, ``uniform`` is used but a warning of the linearisation error is issued.
+Explicitly passing ``hamamatsu_streak_axis_type='uniform'`` suppresses the warning.
+In all cases, the original axis values are stored in the ``original_metadata`` of the
+signal object.
 
 .. code-block:: python
 
     >>> # Force read image resolution using the x_resolution, y_resolution and
-    >>> # the resolution_unit of the TIFF tags. Be aware, that most of the
-    >>> # software doesn't (properly) use these tags when saving TIFF files.
+    >>> # the resolution_unit of the TIFF tags.
     >>> s = hs.load('file.tif', force_read_resolution=True)
+    >>> # Load a non-uniform axis from a hamamatsu streak file:
+    >>> s = hs.load('file.tif', hamamatsu_streak_axis_type='data')
+
+
+Extra saving arguments
+^^^^^^^^^^^^^^^^^^^^^^
 
-HyperSpy can also read and save custom tags through the ``tifffile``
-library.
+- ``extratags`` (tuple, optional): save custom tags through the
+   ``tifffile`` library. Must conform to a specific convention
+   (see ``tifffile`` documentation and example below).
 
 .. code-block:: python
 

hyperspy/io_plugins/sur.py

@@ -577,8 +577,10 @@ def _build_sur_dict(self):
         #If the signal is of the type spectrum or hypercard
         if self._Object_type in ["_HYPCARD",]:
             self._build_hyperspectral_map()
+            #self._build_hyperspectral_signal_type()
         elif self._Object_type in ["_SPECTRUM"]:
             self._build_spectrum()
+            #self._build_spectrum_signal_type()
         elif self._Object_type in ["_PROFILE"]:
             self._build_general_1D_data()
         elif self._Object_type in ["_PROFILESERIE"]: