From 8a4b213829a324c92d519ce2da5a2d05dec38ec5 Mon Sep 17 00:00:00 2001
From: jlaehne <jonas@pdi-berlin.de>
Date: Fri, 3 Jan 2025 10:58:44 +0100
Subject: [PATCH] add time2nav and spec2nav functions

---
 doc/user_guide/streak_images.rst              |  5 ++
 lumispy/hyperspy_extension.yaml               | 12 +++--
 lumispy/signals/luminescence_transientspec.py | 48 +++++++++++++++++++
 3 files changed, 60 insertions(+), 5 deletions(-)

diff --git a/doc/user_guide/streak_images.rst b/doc/user_guide/streak_images.rst
index 0b3113a19..dd3e63538 100644
--- a/doc/user_guide/streak_images.rst
+++ b/doc/user_guide/streak_images.rst
@@ -61,3 +61,8 @@ Similarly, the transient summed over all wavelengths is obtained by:
   :width: 700
   :alt: Plot of a streak camera image and its one-dimensional representations
         obtained by summing over either the wavelength or time dimensions.
+
+
+Iteration over the spectral or time dimension
+=============================================
+
diff --git a/lumispy/hyperspy_extension.yaml b/lumispy/hyperspy_extension.yaml
index 70c77c178..d0f12f0e0 100644
--- a/lumispy/hyperspy_extension.yaml
+++ b/lumispy/hyperspy_extension.yaml
@@ -21,6 +21,7 @@ signals:
     signal_type: Luminescence
     signal_type_aliases:
       - LuminescenceSpectrum
+      - LumiSpectrum
     signal_dimension: 1
     dtype: real
     lazy: False
@@ -29,6 +30,7 @@ signals:
     signal_type: Luminescence
     signal_type_aliases:
       - LuminescenceSpectrum
+      - LumiSpectrum
     signal_dimension: 1
     dtype: real
     lazy: True
@@ -132,9 +134,9 @@ signals:
   LumiTransient:
     signal_type: Transient
     signal_type_aliases:
+      - LumiTransient
       - TRLumi
       - TR luminescence
-      - time-resolved luminescence
     signal_dimension: 1
     dtype: real
     lazy: False
@@ -142,9 +144,9 @@ signals:
   LazyLumiTransient:
     signal_type: Transient
     signal_type_aliases:
+      - LumiTransient
       - TRLumi
       - TR luminescence
-      - time-resolved luminescence
     signal_dimension: 1
     dtype: real
     lazy: True
@@ -153,10 +155,10 @@ signals:
   TransientSpectrumCasting: # allows casting to either Luminescence or Transient when dimensionality is reduced
     signal_type: TransientSpectrum
     signal_type_aliases:
+      - LumiTransientSpectrum
       - TransientSpec
       - TRLumiSpec
       - TR luminescence spectrum
-      - time-resolved luminescence spectrum
     signal_dimension: 1
     dtype: real
     lazy: False
@@ -165,10 +167,10 @@ signals:
   LumiTransientSpectrum:
     signal_type: TransientSpectrum
     signal_type_aliases:
+      - LumiTransientSpectrum
       - TransientSpec
       - TRLumiSpec
       - TR luminescence spectrum
-      - time-resolved luminescence spectrum
     signal_dimension: 2
     dtype: real
     lazy: False
@@ -176,10 +178,10 @@ signals:
   LazyLumiTransientSpectrum:
     signal_type: TransientSpectrum
     signal_type_aliases:
+      - LumiTransientSpectrum
       - TransientSpec
       - TRLumiSpec
       - TR luminescence spectrum
-      - time-resolved luminescence spectrum
     signal_dimension: 2
     dtype: real
     lazy: True
diff --git a/lumispy/signals/luminescence_transientspec.py b/lumispy/signals/luminescence_transientspec.py
index 214ce30ad..c26c0af1a 100644
--- a/lumispy/signals/luminescence_transientspec.py
+++ b/lumispy/signals/luminescence_transientspec.py
@@ -25,6 +25,7 @@
 
 from hyperspy.signals import Signal1D, Signal2D
 from hyperspy._signals.lazy import LazySignal
+from hyperspy.docstrings.signal import OPTIMIZE_ARG
 
 from lumispy.signals import LumiSpectrum, LumiTransient
 from lumispy.signals.common_luminescence import CommonLumi
@@ -69,6 +70,53 @@ class LumiTransientSpectrum(Signal2D, CommonLumi, CommonTransient):
     _signal_type = "TransientSpectrum"
     _signal_dimension = 2
 
+    def spec2nav(self, optimize=True):
+        """Return the streak image as signal with the spectral axis as navigation
+        axis and the time axis as signal axis. For efficient iteration over
+        transients as a function of the spectral positions (e.g. for fitting
+        transients). By default, the method ensures the data is stored optimally,
+        hence often making a copy of the data.
+
+        Parameters
+        ----------
+        %s
+
+        See Also
+        --------
+        lumispy.signals.LumiTransientSpectrum.time2nav
+        hyperspy.api.signals.BaseSignal.transpose
+        """
+        s = self.transpose(signal_axes=[-1],optimize=optimize)
+        return s
+
+    spec2nav.__doc__ %= (
+        OPTIMIZE_ARG.replace("False", "True"),
+    )
+
+    def time2nav(self, optimize=True):
+        """Return the streak image as signal with the time axis as navigation
+        axis and the spectral axis as signal axis. For efficient iteration over
+        spectra as a function of time (e.g. for fitting spectra). By default, the
+        method ensures the data is stored optimally, hence often making a copy
+        of the data.
+
+        Parameters
+        ----------
+        %s
+
+        See Also
+        --------
+        lumispy.signals.LumiTransientSpectrum.time2nav
+        hyperspy.api.signals.BaseSignal.transpose
+        """
+        s = self.transpose(signal_axes=[-2],optimize=optimize)
+        return s
+        #self.axes_manager.signal_axes[-1].navigate = True
+        #self.set_signal_type("LumiSpectrum")
+
+    time2nav.__doc__ %= (
+        OPTIMIZE_ARG.replace("False", "True"),
+    )
 
 class LazyLumiTransientSpectrum(LazySignal, LumiTransientSpectrum):
     """**Lazy 2D luminescence signal class (spectral+transient/time resolved dimensions)**"""