non-uniform updates (NotImplementedErrors, tests, spelling, saving-fix)

hyperspy/_signals/signal1d.py

@@ -513,10 +513,12 @@ def interpolate_in_between(
         Parameters
         ----------
         start, end : int or float
-            The limits of the interval. If int they are taken as the
-            axis index. If float they are taken as the axis value.
+            The limits of the interval. If int, they are taken as the
+            axis index. If float, they are taken as the axis value.
         delta : int or float
-            The windows around the (start, end) to use for interpolation
+            The windows around the (start, end) to use for interpolation. If 
+            int, they are taken as index steps. If float, they are taken in
+            units of the axis value.
         %s
         %s
         %s
@@ -537,9 +539,15 @@ def interpolate_in_between(
         i1 = axis._get_index(start)
         i2 = axis._get_index(end)
         if isinstance(delta, float):
-            delta = int(delta / axis.scale)
-        i0 = int(np.clip(i1 - delta, 0, np.inf))
-        i3 = int(np.clip(i2 + delta, 0, axis.size))
+            if isinstance(start, int):
+                start = axis.axis[start]
+            if isinstance(end, int):
+                end = axis.axis[end]
+            i0 = axis._get_index(start-delta) if start-delta < axis.low_value else 0
+            i3 = axis._get_index(end+delta) if end+delta > axis.high_value else axis.size
+        else:
+            i0 = int(np.clip(i1 - delta, 0, np.inf))
+            i3 = int(np.clip(i2 + delta, 0, axis.size))
 
         def interpolating_function(dat):
             dat_int = interpolate.interp1d(
@@ -616,12 +624,17 @@ def estimate_shift1D(
         ------
         SignalDimensionError
             If the signal dimension is not 1.
+        NotImplementedError
+            If the signal axis is a non-uniform axis.
         """
         if show_progressbar is None:
             show_progressbar = preferences.General.show_progressbar
         self._check_signal_dimension_equals_one()
         ip = number_of_interpolation_points + 1
         axis = self.axes_manager.signal_axes[0]
+        if not axis.is_uniform:
+            raise NotImplementedError(
+                "The function is not implemented for non-uniform signal axes.")
         self._check_navigation_mask(mask)
         # we compute for now
         if isinstance(start, da.Array):
@@ -863,6 +876,8 @@ def calibrate(self, display=True, toolkit=None):
         ------
         SignalDimensionError
             If the signal dimension is not 1.
+        NotImplementedError
+            If called with a non-uniform axes.
         """
         self._check_signal_dimension_equals_one()
         calibration = Signal1DCalibration(self)

hyperspy/component.py

@@ -1245,7 +1245,7 @@ def print_current_values(self, only_free=False, fancy=True):
 def _get_scaling_factor(signal, axis, parameter):
     """
     Convenience function to get the scaling factor required to take into
-    account binned and/or non uniform axes.
+    account binned and/or non-uniform axes.
 
     Parameters
     ----------

hyperspy/datasets/artificial_data.py

@@ -452,10 +452,10 @@ def get_luminescence_signal(navigation_dimension=0,
     if add_baseline:
         data += 350.
 
-    #if not uniform, transformation into non-linear axis
+    #if not uniform, transformation into non-uniform axis
     if not uniform:
         hc = 1239.84198 #nm/eV
-        #converting to non uniform axis
+        #converting to non-uniform axis
         sig.axes_manager.signal_axes[0].convert_to_functional_data_axis(\
                                                               expression="a/x",
                                                               name='Energy',

hyperspy/io.py

@@ -753,6 +753,7 @@ def save(filename, signal, overwrite=None, **kwds):
     # Check if the writer can write
     sd = signal.axes_manager.signal_dimension
     nd = signal.axes_manager.navigation_dimension
+    nua = signal.axes_manager.all_uniform
 
     if writer.writes is False:
         raise ValueError(
@@ -771,6 +772,14 @@ def save(filename, signal, overwrite=None, **kwds):
             f"Please try one of {strlist2enumeration(yes_we_can)}"
         )
 
+    if writer.non_uniform_axis is False and nua is False:
+        yes_we_can = [plugin.format_name for plugin in io_plugins
+                      if plugin.non_uniform_axis is True]
+        raise OSError("Writing to this format is not supported for "
+                      "non-uniform axes. Use one of the following "
+                      f"formats: {strlist2enumeration(yes_we_can)}"
+        )
+
     # Create the directory if it does not exist
     ensure_directory(filename.parent)
     is_file = filename.is_file()
@@ -782,40 +791,8 @@ def save(filename, signal, overwrite=None, **kwds):
     elif overwrite is False and is_file:
         write = False  # Don't write the file
     else:
-        # Check if the writer can write
-        sd = signal.axes_manager.signal_dimension
-        nd = signal.axes_manager.navigation_dimension
-        nua = signal.axes_manager.all_uniform
-        if writer.writes is False:
-            raise ValueError('Writing to this format is not '
-                             'supported, supported file extensions are: %s ' %
-                             strlist2enumeration(default_write_ext))
-        if writer.writes is not True and (sd, nd) not in writer.writes:
-            yes_we_can = [plugin.format_name for plugin in io_plugins
-                          if plugin.writes is True or
-                          plugin.writes is not False and
-                          (sd, nd) in plugin.writes]
-            raise IOError('This file format cannot write this data. '
-                          'The following formats can: %s' %
-                          strlist2enumeration(yes_we_can))
-        if writer.non_uniform_axis is False and nua is False:
-            yes_we_can = [plugin.format_name for plugin in io_plugins
-                          if plugin.non_uniform_axis is True]
-            raise OSError('Writing to this format is not supported for non '
-                          'uniform axes.'
-                          'Use one of the following formats: %s' %
-                          strlist2enumeration(yes_we_can))
-        ensure_directory(filename)
-        is_file = os.path.isfile(filename)
-        if overwrite is None:
-            write = overwrite_method(filename)  # Ask what to do
-        elif overwrite is True or (overwrite is False and not is_file):
-            write = True  # Write the file
-        elif overwrite is False and is_file:
-            write = False  # Don't write the file
-        else:
-            raise ValueError("`overwrite` parameter can only be None, True or "
-                             "False.")
+        raise ValueError("`overwrite` parameter can only be None, True or "
+                         "False.")
     if write:
         # Pass as a string for now, pathlib.Path not
         # properly supported in io_plugins

hyperspy/io_plugins/README

@@ -21,8 +21,8 @@ All the read/write plugins must provide a python file containing:
         writes_images = <Bool>
         writes_spectrum = <Bool>
         writes_spectrum_image = <Bool>
-        # Support for non linear axis
-        non_linear_axis = <Bool>
+        # Support for non-uniform axis
+        non_uniform_axis = <Bool>
 
     - A function called file_reader with at least one attribute: filename
 

hyperspy/io_plugins/emd.py

@@ -684,7 +684,7 @@ def _read_data_from_groups(self, group_path, dataset_name, stack_key=None,
                                    simu_om.get('cellDimension', 0)[0])
                 if not math.isclose(total_thickness, len(array_list) * scale,
                                     rel_tol=1e-4):
-                    _logger.warning("Depth axis is non uniform and its offset "
+                    _logger.warning("Depth axis is non-uniform and its offset "
                                     "and scale can't be set accurately.")
                     # When non-uniform/non-linear axis are implemented, adjust
                     # the final depth to the "total_thickness"
@@ -798,7 +798,7 @@ def _parse_axis(axis_data):
             offset, scale = axis_data[0], np.diff(axis_data).mean()
         else:
             # This is a string, return default values
-            # When non-linear axis is supported we should be able to parse
+            # When non-uniform axis is supported we should be able to parse
             # string
             offset, scale = 0, 1
         return offset, scale

hyperspy/io_plugins/hspy.py

@@ -79,7 +79,7 @@
 # CHANGES
 #
 # v3.1
-# - add read support for non-linear DataAxis defined by 'axis' vector
+# - add read support for non-uniform DataAxis defined by 'axis' vector
 # - move metadata.Signal.binned attribute to axes.is_binned parameter
 #
 # v3.0

hyperspy/io_plugins/jeol.py

@@ -42,6 +42,8 @@
 reads_spectrum_image = True
 # Writing capabilities
 writes = False
+non_uniform_axis = False
+# ----------------------
 
 
 jTYPE = {
@@ -724,4 +726,4 @@ def read_eds(filename, **kwargs):
 extension_to_reader_mapping = {"img": read_img,
                                "map": read_img,
                                "pts": read_pts,
-                               "eds": read_eds}
+                               "eds": read_eds}

hyperspy/models/model1d.py

@@ -319,7 +319,7 @@ def low_loss(self, value):
                                  'navigation dimension as the core-loss.')
             if not value.axes_manager.signal_axes[0].is_uniform:
                 raise ValueError('Low loss convolution is not supported with '
-                                 'non linear signal axes.')
+                                 'non-uniform signal axes.')
             self._low_loss = value
             self.set_convolution_axis()
             self.convolved = True

hyperspy/signal_tools.py

@@ -201,7 +201,7 @@ def __init__(self, signal):
             raise SignalDimensionError(
                 signal.axes_manager.signal_dimension, 1)
         if not isinstance(self.axis, UniformDataAxis):
-            raise ValueError("The calibration tool supports only uniform axes.")
+            raise NotImplementedError("The calibration tool supports only uniform axes.")
         self.units = self.axis.units
         self.scale = self.axis.scale
         self.offset = self.axis.offset

hyperspy/tests/io/test_io.py

@@ -87,6 +87,10 @@ def test_io_overwriting_None_existing_file_n(self):
             self.new_s.save(FULLFILENAME)
             assert not self._check_file_is_written(FULLFILENAME)
 
+    def test_io_overwriting_invalid_parameter(self):
+        with pytest.raises(ValueError, match="parameter can only be"):
+            self.new_s.save(FULLFILENAME, overwrite="spam")
+
     def teardown_method(self, method):
         self._clean_file()
 
@@ -100,7 +104,7 @@ def setup_method(self, method):
     def test_io_nonuniform(self):
         assert(self.s.axes_manager[0].is_uniform == False)
         self.s.save('tmp.hspy', overwrite = True)
-        with pytest.raises(AttributeError):
+        with pytest.raises(OSError):
             self.s.save('tmp.msa', overwrite = True)
 
     def test_nonuniform_writer_characteristic(self):
@@ -111,6 +115,17 @@ def test_nonuniform_writer_characteristic(self):
                 print(plugin.format_name + ' IO-plugin is missing the '
                       'characteristic `non_uniform_axis`')
 
+    def test_nonuniform_error(self):
+        assert(self.s.axes_manager[0].is_uniform == False)
+        no_we_cant = [plugin.file_extensions[plugin.default_extension] for
+                      plugin in io_plugins if (plugin.writes is True or
+                      plugin.writes is not False and (1, 0) in plugin.writes)
+                      and plugin.non_uniform_axis is False]
+        for ext in no_we_cant:
+            with pytest.raises(OSError, match = "not supported for"):
+                filename = 'tmp.' + ext
+                self.s.save(filename, overwrite = True)
+
     def teardown_method(self):
         if os.path.exists('tmp.hspy'):
             os.remove('tmp.hspy')

hyperspy/tests/signals/test_1D_tools.py

@@ -218,11 +218,26 @@ def test_single_spectrum(self):
         np.testing.assert_array_equal(s.data, np.arange(20))
         assert m.data_changed.called
 
+    def test_single_spectrum_nonuniform(self):
+        s = self.s.inav[0]
+        m = mock.Mock()
+        s.events.data_changed.connect(m.data_changed)
+        s.axes_manager[-1].convert_to_non_uniform_axis()
+        s.interpolate_in_between(8, 12)
+        np.testing.assert_array_equal(s.data, np.arange(20))
+        assert m.data_changed.called
+
     def test_single_spectrum_in_units(self):
         s = self.s.inav[0]
         s.interpolate_in_between(0.8, 1.2)
         np.testing.assert_array_equal(s.data, np.arange(20))
 
+    def test_single_spectrum_in_units_nonuniform(self):
+        s = self.s.inav[0]
+        s.axes_manager[-1].convert_to_non_uniform_axis()
+        s.interpolate_in_between(0.8, 1.2)
+        np.testing.assert_array_equal(s.data, np.arange(20))
+
     def test_two_spectra(self):
         s = self.s
         s.interpolate_in_between(8, 12)
@@ -248,8 +263,23 @@ def test_delta_float(self):
         s.interpolate_in_between(8, 12, delta=0.31, kind='cubic')
         print(s.data[8:12])
         np.testing.assert_allclose(
-            s.data[8:12], np.array([45.09388598, 104.16170809,
-                                    155.48258721, 170.33564422]),
+            s.data[8:12], np.array([46.595205, 109.802805, 
+                                    164.512803, 178.615201]),
+            atol=1,
+        )
+
+    def test_delta_float_nonuniform(self):
+        s = self.s.inav[0]
+        s.change_dtype('float')
+        tmp = np.zeros(s.data.shape)
+        tmp[12] = s.data[12]
+        s.data += tmp * 9.
+        s.axes_manager[0].convert_to_non_uniform_axis()
+        s.interpolate_in_between(8, 12, delta=0.31, kind='cubic')
+        print(s.data[8:12])
+        np.testing.assert_allclose(
+            s.data[8:12], np.array([46.595205, 109.802805, 
+                                    164.512803, 178.615201]),
             atol=1,
         )
 

hyperspy/tests/test_non-uniform_not-implemented.py

@@ -41,8 +41,12 @@ def test_signal():
 def test_signal1d():
     s = Signal1D((1))
     s.axes_manager[0].convert_to_non_uniform_axis()
+    with pytest.raises(NotImplementedError):
+        s.calibrate()
     with pytest.raises(NotImplementedError):
         s.shift1D([1])
+    with pytest.raises(NotImplementedError):
+        s.estimate_shift1D([1])
     with pytest.raises(NotImplementedError):
         s.smooth_savitzky_golay()
     with pytest.raises(NotImplementedError):