implement suggestions from code review

conda_environment_dev.yml

@@ -7,6 +7,6 @@ dependencies:
 - pytest-cov
 - pytest-faulthandler
 - pytest-xdist
-- hyperspy[speed]
+- hyperspy-base
 - setuptools-scm
 

doc/user_guide/fitting_luminescence.rst

@@ -32,7 +32,6 @@ Signal variance (noise)
 =======================
 
 TODO: Documentation on variance handling in the context of fitting,
-in particular using :external:meth:`estimate_poissonian_noise_variance()
-<hyperspy.api.signals.BaseSignal.estimate_poissonian_noise_variance>`
+in particular using :external:meth:`~hyperspy.api.signals.BaseSignal.estimate_poissonian_noise_variance`
 
 For a detailed discussion, see [Tappy]_

doc/user_guide/signal_axis.rst

@@ -9,10 +9,10 @@ occurs in particular when converting a wavelength scale to energy (eV) or
 wavenumbers (e.g. for Raman shifts).
 
 The conversion of the signal axis can be performed using the functions 
-:meth:`~.signals.luminescence_spectrum.LumiSpectrum.to_eV`,
-:meth:`~.signals.luminescence_spectrum.LumiSpectrum.to_invcm` and
-:meth:`~.signals.luminescence_spectrum.LumiSpectrum.to_raman_shift`
-(alias for :meth:`~.signals.luminescence_spectrum.LumiSpectrum.to_invcm_relative`).
+:meth:`~.signals.common_luminescence.CommonLumi.to_eV`,
+:meth:`~.signals.common_luminescence.CommonLumi.to_invcm` and
+:meth:`~.signals.common_luminescence.CommonLumi.to_raman_shift`
+(alias for :meth:`~.signals.common_luminescence.CommonLumi.to_invcm_relative`).
 If the unit of the signal axis is set, the functions can handle wavelengths in
 either nm or µm.
 
@@ -123,7 +123,7 @@ renormalization is automatically performed by LumiSpy if ``jacobian=True``.
 In particular, homoscedastic (constant) noise will consequently become
 heteroscedastic (changing as a function of the signal axis vector). Therefore,
 if the ``metadata.Signal.Noise_properties.variance`` attribute is a constant,
-it is converted into a :external:class:` BaseSignal <hyperspy.api.signals.BaseSignal>`
+it is converted into a :external:class:`hyperspy.api.signals.BaseSignal`
 object before the transformation.
 
 See the section on :ref:`fitting_variance` for more general information on data variance
@@ -136,8 +136,7 @@ in the context of model fitting and the HyperSpy documentation on `
     ``metadata.Signal.Noise_properties.Variance_linear_model`` are reset to
     their default values (``gain_factor=1``, ``gain_offset=0`` and ``correlation_factor=1``).
     Should these values deviate from the defaults, make sure to run
-    :external:meth:`estimate_poissonian_noise_variance()
-    <hyperspy.api.signals.BaseSignal.estimate_poissonian_noise_variance>`
+    :external:meth:`~hyperspy.api.signals.BaseSignal.estimate_poissonian_noise_variance`
     prior to the transformation.
 
 
@@ -147,8 +146,8 @@ Interpolation to uniform axes
 =============================
 
 As a number of HyperSpy tools are not supporting non-uniform axes, e.g. the
-:meth:`rebin() <hyperspy.api.signals.BaseSignal.rebin>` function, the HyperSpy function
-:meth:`interpolate_on_axis() <hyperspy.api.signals.BaseSignal.interpolate_on_axis>`
+:meth:`~hyperspy.api.signals.BaseSignal.rebin` function, the HyperSpy function
+:meth:`~hyperspy.api.signals.BaseSignal.interpolate_on_axis`
 provides a possibility to convert a signal with a non-uniform axis to one with
 a uniform axis. This function takes the argument ``"uniform"``, which will create
 a signal with the same number of data points, but a uniform axes spacing and

doc/user_guide/signal_tools.rst

@@ -53,14 +53,14 @@ Peak identification
 HyperSpy provides functions to find the positions of maxima or minima in a
 dataset:
 
-- :external:meth:`indexmax() <hyperspy.api.signals.BaseSignal.indexmax>` - 
+- :external:meth:`~hyperspy.api.signals.BaseSignal.indexmax` - 
   return the index of the maximum value along a given axis.
-- :external:meth:`indexmin() <hyperspy.api.signals.BaseSignal.indexmin>` - 
+- :external:meth:`~hyperspy.api.signals.BaseSignal.indexmin` - 
   return the index of the minimum value along a given axis.
-- :external:meth:`valuemax() <hyperspy.api.signals.BaseSignal.valuemax>` - 
+- :external:meth:`~hyperspy.api.signals.BaseSignal.valuemax` - 
   return the position/coordinates of the maximum value along a given axis in
   calibrated units.
-- :external:meth:`valuemin() <hyperspy.api.signals.BaseSignal.valuemin>` - 
+- :external:meth:`~hyperspy.api.signals.BaseSignal.valuemin` - 
   return the position/coordinates of the minimum value along a given axis in
   calibrated units.
 
@@ -69,7 +69,7 @@ the operation and return a new signal containing the result.
 
 A much more powerful method to identify peaks is using the **peak finding routine**
 based on the downward zero-crossings of the first derivative of a signal:
-:external:meth:`find_peaks1D_ohaver() <hyperspy.api.signals.Signal1D.find_peaks1D_ohaver>`.
+:external:meth:`~hyperspy.api.signals.Signal1D.find_peaks1D_ohaver`.
 This function can find multiple peaks in a dataset and has a number of parameters
 for fine-tuning the sensitivity, etc.
 
@@ -87,7 +87,7 @@ Peak Width
 
 For asymmetric peaks, :ref:`fitted functions <fitting_luminescence>` may not provide
 an accurate description of the peak, in particular the peak width. The function
-:external:meth:`estimate_peak_width() <hyperspy.api.signals.Signal1D.estimate_peak_width>`
+:external:meth:`~hyperspy.api.signals.Signal1D.estimate_peak_width`
 determines the **width of a peak** at a certain fraction of its maximum value. The
 default value ``factor=0.5`` returns the full width at half maximum (FWHM).
 
@@ -158,23 +158,23 @@ Signal statistics and analytical operations
 ===========================================
 
 **Standard statistical operations** can be performed on the data or a subset of the
-data, notably these include 
-:external:meth:`max() <hyperspy.api.signals.BaseSignal.max>`,
-:external:meth:`min() <hyperspy.api.signals.BaseSignal.min>`,
-:external:meth:`sum() <hyperspy.api.signals.BaseSignal.sum>`,
-:external:meth:`mean() <hyperspy.api.signals.BaseSignal.mean>`,
-:external:meth:`std() <hyperspy.api.signals.BaseSignal.std>`, and
-:external:meth:`var() <hyperspy.api.signals.BaseSignal.var>`. Variations of
+data using HyperSpy methods, notably these include 
+:external:meth:`~hyperspy.api.signals.BaseSignal.max`,
+:external:meth:`~hyperspy.api.signals.BaseSignal.min`,
+:external:meth:`~hyperspy.api.signals.BaseSignal.sum`,
+:external:meth:`~hyperspy.api.signals.BaseSignal.mean`,
+:external:meth:`~hyperspy.api.signals.BaseSignal.std`, and
+:external:meth:`~hyperspy.api.signals.BaseSignal.var`. Variations of
 all these functions exist that ignore missing values (NaN) if present, e.g.
-:external:meth:`nanmax() <hyperspy.api.signals.BaseSignal.nanmax>`.
+:external:meth:`~hyperspy.api.signals.BaseSignal.nanmax`.
 
 **Integration** along a specified signal axis is performed using the function 
-:external:meth:`integrate1D() <hyperspy.api.signals.BaseSignal.integrate1D()>`.
+:external:meth:`~hyperspy.api.signals.BaseSignal.integrate1D()`.
 
 The numerical **derivative** of a signal can be calculated using the function
-:external:meth:`derivative() <hyperspy.api.signals.BaseSignal.derivative()>`,
+:external:meth:`~hyperspy.api.signals.BaseSignal.derivative()`,
 while the *n*-th order **discrete difference** can be calculated using
-:external:meth:`diff() <hyperspy.api.signals.BaseSignal.diff()>`.
+:external:meth:`~hyperspy.api.signals.BaseSignal.diff()`.
 
 These functions take the ``axis`` keyword to define along which axis to perform
 the operation and return a new signal containing the result:

doc/user_guide/streak_images.rst

@@ -12,8 +12,8 @@ wavelength axis can be transformed to e.g. a :ref:`energy_axis`.
 
 .. Note::
 
-    For streak images, not all tools available for :class:`Signal2D
-    <hyperspy.api.signals.Signal2D>` will work. However, in particular
+    For streak images, not all tools available for :class:`hyperspy.api.signals.Signal2D`
+    will work. However, in particular
     :external+hyperspy:ref:`peak_finding-label`
     can be helpful to identify local maxima in the images.
 
@@ -27,25 +27,35 @@ assign the correct 1D signal class: Either :class:`~.signals.luminescence_spectr
 :class:`~.signals.luminescence_transient.LumiTransient`. Such a reduction of the signal dimensionality
 can be done for example by slicing the signal with
 :external+hyperspy:ref:`numpy-style indexing <signal.indexing>` or by using
-functions such as :external:meth:`sum() <hyperspy.api.signals.BaseSignal.sum>`
-and :external:meth:`integrate1D() <hyperspy.api.signals.BaseSignal.integrate1D>`
+functions such as :external:meth:`~hyperspy.api.signals.BaseSignal.sum`
+and :external:meth:`~hyperspy.api.signals.BaseSignal.integrate1D`
 
 In the following image, the spectrum summed over all times is obtained from the
 streak image by:
 
 .. code-block:: python
 
-    >>> s.sum(axis='Time')
-    >>> # Or alternatively:
-    >>> s.sum(axis=-1)
+    import lumispy as lum
+    import numpy as np
+    
+    data = np.arange(10*20).reshape(10, 20)
+    
+    s = lum.signals.LumiTransientSpectrum(data)
+    s.axes_manager[-1].name = "Time"
+    s.axes_manager[-1].units = "ns"
+    s.axes_manager[-2].name = "Wavelength"
+    s.axes_manager[-2].units = "nm"
+    s.sum(axis='Time')
+    # Or alternatively:
+    s.sum(axis=-1)
 
 Similarly, the transient summed over all wavelengths is obtained by:
 
 .. code-block:: python
 
-    >>> s.sum(axis='Wavelength')
-    >>> # Or alternatively:
-    >>> s.sum(axis=-2)
+    s.sum(axis='Wavelength')
+    # Or alternatively:
+    s.sum(axis=-2)
 
 .. image:: images/streakmap.svg
   :width: 700

upcoming_changes/205.new.rst

@@ -1 +1 @@
-Implement correct casting of :class:`~.signals.luminescence_transientspec.LumiTransientSpectrum` to either :class:`~.signals.luminescence_spectrum.LumiSpectrum` or :class:`~.signals.luminescence_transient.LumiTransient` when the signal dimension is reduced
+Implement correct casting of :class:`~.signals.luminescence_transientspec.LumiTransientSpectrum` to either :class:`~.signals.luminescence_spectrum.LumiSpectrum` or :class:`~.signals.luminescence_transient.LumiTransient` when the signal dimension is reduced - previously, a :class:`~hyperspy.api.signals.Signal1D` object was returned.