Fix: Add "Replace X by other signal's Y" for calibration workflows

PierreRaybaut · PierreRaybaut · commit 49d03bc6d5b9 · 2025-12-03T13:16:03.000+01:00
Fixes #273
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,22 @@ See DataLab [roadmap page](https://datalab-platform.com/en/contributing/roadmap.
 
 ### 🛠️ Bug Fixes ###
 
+**Signal axis calibration - Replace X by other signal's Y:**
+
+* Added new "Replace X by other signal's Y" operation in Processing > Axis transformation menu for signal calibration workflows
+* Addresses critical missing functionality reported by users who needed to apply wavelength calibration or similar transformations to spectroscopy data
+* The operation combines two signals: uses Y values from one signal as the new X coordinates for another signal's Y values
+* Unlike X-Y mode (which resamples and interpolates), this operation directly uses Y arrays without interpolation, preserving exact calibration values
+* Requires both signals to have the same number of points - raises clear error message if sizes don't match
+* Automatically transfers metadata: X axis label/unit taken from calibration signal's Y label/unit
+* Menu location: Processing > Axis transformation > "Replace X by other signal's Y"
+* This closes [Issue #273](https://github.com/datalab-platform/datalab/issues/273) - Missing signal axis calibration: no way to replace X with Y from another signal
+
+**X-Y mode:**
+
+* The X-Y mode processing operation for signals has been moved to Processing > Axis transformation > "X-Y mode" for better discoverability
+* The nuance between X-Y mode (which resamples/interpolates) and the new "Replace X by other signal's Y" operation has been clarified in documentation
+
 **Lock LUT setting persistence:**
 
 * Fixed "Lock LUT range when updating data" setting not persisting in Settings > Visualization > Images > Default Image visualization settings
diff --git a/datalab/gui/actionhandler.py b/datalab/gui/actionhandler.py
@@ -1269,7 +1269,9 @@ def cra_fit(title, fitdlgfunc, tip: str | None = None):
             with self.new_menu(_("Axis transformation")):
                 self.action_for("transpose")
                 self.action_for("reverse_x")
-                self.action_for("to_cartesian")
+                self.action_for("replace_x_by_other_y")
+                self.action_for("xy_mode")
+                self.action_for("to_cartesian", separator=True)
                 self.action_for("to_polar")
             with self.new_menu(_("Frequency filters"), icon_name="highpass.svg"):
                 self.action_for("lowpass")
@@ -1364,7 +1366,6 @@ def cra_fit(title, fitdlgfunc, tip: str | None = None):
                     separator=True,
                     tip=_("Compute all stability features"),
                 )
-            self.action_for("xy_mode", separator=True)
 
         # MARK: ANALYSIS
         with self.new_category(ActionCategory.ANALYSIS):
diff --git a/datalab/gui/processor/signal.py b/datalab/gui/processor/signal.py
@@ -164,6 +164,16 @@ def register_operations(self) -> None:
             icon_name="convolution.svg",
             obj2_name=_("signal to convolve with"),
         )
+        self.register_2_to_1(
+            sips.replace_x_by_other_y,
+            _("Replace X by other signal's Y"),
+            comment=_(
+                "Replace X coordinates using Y values from another signal.\n"
+                "Useful for calibration: plot data vs wavelength scale."
+            ),
+            obj2_name=_("signal providing Y values for X axis"),
+            skip_xarray_compat=True,
+        )
         self.register_2_to_1(
             sips.deconvolution,
             _("Deconvolution"),
diff --git a/datalab/locale/fr/LC_MESSAGES/datalab.po b/datalab/locale/fr/LC_MESSAGES/datalab.po
@@ -6,7 +6,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version:  datalab\n"
 "Report-Msgid-Bugs-To: p.raybaut@codra.fr\n"
-"POT-Creation-Date: 2025-11-29 16:49+0100\n"
+"POT-Creation-Date: 2025-12-03 12:01+0100\n"
 "PO-Revision-Date: 2025-05-22 15:46+0200\n"
 "Last-Translator: Christophe Debonnel <c.debonnel@codra.fr>\n"
 "Language: fr\n"
@@ -1891,6 +1891,19 @@ msgstr "Intégrale"
 msgid "signal to convolve with"
 msgstr "signal pour la convolution"
 
+msgid "Replace X by other signal's Y"
+msgstr "Remplacer X par le Y d'un autre signal"
+
+msgid ""
+"Replace X coordinates using Y values from another signal.\n"
+"Useful for calibration: plot data vs wavelength scale."
+msgstr ""
+"Remplacer les coordonnées X en utilisant les valeurs Y d'un autre signal.\n"
+"Utile pour l'étalonnage : tracer des données en fonction d'une échelle de longueurs d'onde."
+
+msgid "signal providing Y values for X axis"
+msgstr "signal fournissant les valeurs Y pour l'axe X"
+
 msgid "signal to deconvolve with"
 msgstr "signal pour la déconvolution"
 
diff --git a/doc/features/signal/menu_processing.rst b/doc/features/signal/menu_processing.rst
@@ -51,6 +51,48 @@ Reverse X-axis
 
 Create a new signal which is the result of reversing X data.
 
+Replace X by other signal's Y
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Create a new signal by combining two signals, using Y values from the second signal
+as X coordinates for the first signal's Y values.
+
+This feature is particularly useful for calibration scenarios, such as:
+
+- Applying wavelength calibration to spectroscopy data
+- Using a calibrated reference signal to rescale measurement data
+- Combining signals where one contains calibration points
+
+The two signals must have the same number of points. The operation directly uses
+the Y arrays without interpolation.
+
+.. list-table::
+    :header-rows: 1
+    :widths: 40, 60
+
+    * - Input
+      - Description
+    * - Signal 1
+      - Provides the Y data for the output signal
+    * - Signal 2
+      - Provides the Y data that becomes the X coordinates of the output signal
+
+X-Y mode
+~~~~~~~~
+
+Create a new signal by simulating the X-Y mode of an oscilloscope.
+
+This operation plots one signal as a function of another by:
+
+1. Finding the overlapping X range between both signals
+2. Resampling both signals onto a common X grid within that overlap
+3. Using the resampled Y values as coordinates (first signal's Y as X, second signal's Y as Y)
+
+.. note::
+
+  This is different from "Replace X by other signal's Y" as it performs interpolation to handle signals
+  with different X arrays.
+
 Convert to Cartesian coordinates
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -481,9 +523,3 @@ The following stability analysis methods are available:
 .. note::
 
     The "All stability features" option allows to compute all stability analysis methods at once.
-
-
-X-Y Mode
-^^^^^^^^
-
-Simulate the X-Y mode of an oscilloscope.
diff --git a/doc/intro/keyfeatures.rst b/doc/intro/keyfeatures.rst
@@ -61,13 +61,14 @@ Signal Image  Feature
 ✓      ✓      Linear calibration
 ✓      ✓      Normalization, Clipping, Offset correction
 ✓      ..     Reverse X-axis
+✓      ..     Replace X by other signal's Y (calibration)
+✓      ..     X-Y mode
 ..     ✓      Thresholding (manual, Otsu...)
 ✓      ✓      Gaussian filter, Wiener filter
 ✓      ✓      Moving average, moving median
 ✓      ✓      FFT, inverse FFT, Power/Phase/Magnitude spectrum, Power Spectral Density
 ✓      ..     Interpolation, resampling
 ✓      ..     Detrending
-✓      ..     X-Y mode
 ✓      ..     Interactive fit: Gauss, Lorentz, Voigt, polynomial, CDF...
 ✓      ..     Interactive multigaussian fit
 ✓      ..     Frequency filters (low-pass, high-pass, band-pass, band-stop)
diff --git a/doc/locale/fr/LC_MESSAGES/changelog.po b/doc/locale/fr/LC_MESSAGES/changelog.po
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: DataLab \n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2025-11-30 15:30+0100\n"
+"POT-Creation-Date: 2025-12-03 12:01+0100\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language: fr\n"
@@ -30,6 +30,42 @@ msgstr "DataLab Version 1.0.2 (non publiée)"
 msgid "🛠️ Bug Fixes"
 msgstr "🛠️ Correctifs"
 
+msgid "**Signal axis calibration - Replace X by other signal's Y:**"
+msgstr "**Calibration de l'axe des signaux - Remplacer X par le Y d'un autre signal :**"
+
+msgid "Added new \"Replace X by other signal's Y\" operation in Processing > Axis transformation menu for signal calibration workflows"
+msgstr "Ajout de la nouvelle opération \"Remplacer X par le Y d'un autre signal\" dans le menu Traitement > Transformation d'axe pour les flux de travail de calibration des signaux"
+
+msgid "Addresses critical missing functionality reported by users who needed to apply wavelength calibration or similar transformations to spectroscopy data"
+msgstr "Répond à une fonctionnalité critique manquante signalée par les utilisateurs qui avaient besoin d'appliquer une calibration en longueur d'onde ou des transformations similaires aux données de spectroscopie"
+
+msgid "The operation combines two signals: uses Y values from one signal as the new X coordinates for another signal's Y values"
+msgstr "L'opération combine deux signaux : elle utilise les valeurs Y d'un signal comme nouvelles coordonnées X pour les valeurs Y d'un autre signal"
+
+msgid "Unlike X-Y mode (which resamples and interpolates), this operation directly uses Y arrays without interpolation, preserving exact calibration values"
+msgstr "Contrairement au mode X-Y (qui rééchantillonne et interpole), cette opération utilise directement les tableaux Y sans interpolation, préservant ainsi les valeurs de calibration exactes"
+
+msgid "Requires both signals to have the same number of points - raises clear error message if sizes don't match"
+msgstr "Nécessite que les deux signaux aient le même nombre de points - affiche un message d'erreur clair si les tailles ne correspondent pas"
+
+msgid "Automatically transfers metadata: X axis label/unit taken from calibration signal's Y label/unit"
+msgstr "Transfert automatique des métadonnées : l'étiquette/unité de l'axe X est prise à partir de l'étiquette/unité Y du signal de calibration"
+
+msgid "Menu location: Processing > Axis transformation > \"Replace X by other signal's Y\""
+msgstr "Emplacement dans le menu : Traitement > Transformation d'axe > \"Remplacer X par le Y d'un autre signal\""
+
+msgid "This closes [Issue #273](https://github.com/datalab-platform/datalab/issues/273) - Missing signal axis calibration: no way to replace X with Y from another signal"
+msgstr "Ceci clôture [Issue #273](https://github.com/datalab-platform/datalab/issues/273) - Calibration de l'axe des signaux manquante : aucun moyen de remplacer X par Y d'un autre signal"
+
+msgid "**X-Y mode:**"
+msgstr "**Mode X-Y :**"
+
+msgid "The X-Y mode processing operation for signals has been moved to Processing > Axis transformation > \"X-Y mode\" for better discoverability"
+msgstr "Le traitement Mode X-Y pour les signaux a été déplacé vers Traitement > Transformation des axes > \"Mode X-Y\" pour une meilleure découvrabilité"
+
+msgid "The nuance between X-Y mode (which resamples/interpolates) and the new \"Replace X by other signal's Y\" operation has been clarified in documentation"
+msgstr "La nuance entre le mode X-Y (qui rééchantillonne/interpole) et la nouvelle opération \"Remplacer X par le Y d'un autre signal\" a été clarifiée dans la documentation"
+
 msgid "**Lock LUT setting persistence:**"
 msgstr "**Persistance du paramètre de verrouillage de la LUT :**"
 
diff --git a/doc/locale/fr/LC_MESSAGES/features/signal/menu_processing.po b/doc/locale/fr/LC_MESSAGES/features/signal/menu_processing.po
@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: DataLab \n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2025-10-27 18:12+0100\n"
+"POT-Creation-Date: 2025-12-03 11:35+0100\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language: fr\n"
@@ -75,6 +75,66 @@ msgstr "Inverser l'axe des X"
 msgid "Create a new signal which is the result of reversing X data."
 msgstr "Crée un signal à partir des données inversées de l'axe des X du signal sélectionné."
 
+msgid "Replace X by other signal's Y"
+msgstr "Remplacer X par le Y d'un autre signal"
+
+msgid "Create a new signal by combining two signals, using Y values from the second signal as X coordinates for the first signal's Y values."
+msgstr "Crée un nouveau signal en combinant deux signaux, en utilisant les valeurs Y du second signal comme coordonnées X pour les valeurs Y du premier signal."
+
+msgid "This feature is particularly useful for calibration scenarios, such as:"
+msgstr "Cette fonctionnalité est particulièrement utile pour les scénarios d'étalonnage, tels que :"
+
+msgid "Applying wavelength calibration to spectroscopy data"
+msgstr "Appliquer un étalonnage en longueur d'onde aux données de spectroscopie"
+
+msgid "Using a calibrated reference signal to rescale measurement data"
+msgstr "Utiliser un signal de référence étalonné pour recalibrer les données de mesure"
+
+msgid "Combining signals where one contains calibration points"
+msgstr "Combiner des signaux où l'un contient des points d'étalonnage"
+
+msgid "The two signals must have the same number of points. The operation directly uses the Y arrays without interpolation."
+msgstr "Les deux signaux doivent avoir le même nombre de points. L'opération utilise directement les tableaux Y sans interpolation."
+
+msgid "Input"
+msgstr "Entrée"
+
+msgid "Description"
+msgstr "Description"
+
+msgid "Signal 1"
+msgstr "Signal 1"
+
+msgid "Provides the Y data for the output signal"
+msgstr "Fournit les données Y pour le signal de sortie"
+
+msgid "Signal 2"
+msgstr "Signal 2"
+
+msgid "Provides the Y data that becomes the X coordinates of the output signal"
+msgstr "Fournit les données Y qui deviennent les coordonnées X du signal de sortie"
+
+msgid "X-Y mode"
+msgstr "Mode X-Y"
+
+msgid "Create a new signal by simulating the X-Y mode of an oscilloscope."
+msgstr "Crée un nouveau signal en simulant le mode X-Y d'un oscilloscope."
+
+msgid "This operation plots one signal as a function of another by:"
+msgstr "Cette opération trace un signal en fonction d'un autre en :"
+
+msgid "Finding the overlapping X range between both signals"
+msgstr "Trouvant la plage X qui se chevauche entre les deux signaux"
+
+msgid "Resampling both signals onto a common X grid within that overlap"
+msgstr "Rééchantillonnant les deux signaux sur une grille X commune dans ce chevauchement"
+
+msgid "Using the resampled Y values as coordinates (first signal's Y as X, second signal's Y as Y)"
+msgstr "Utilisant les valeurs Y rééchantillonnées comme coordonnées (Y du premier signal comme X, Y du second signal comme Y)"
+
+msgid "This is different from \"Replace X by other signal's Y\" as it performs interpolation to handle signals with different X arrays."
+msgstr "Ceci est différent de \"Remplacer X par le Y d'un autre signal\" car il effectue une interpolation pour gérer les signaux avec des tableaux X différents."
+
 msgid "Convert to Cartesian coordinates"
 msgstr "Convertir en coordonnées cartésiennes"
 
@@ -108,7 +168,6 @@ msgstr "Normalisation"
 msgid "Maximum"
 msgstr "Maximum"
 
-#, python-brace-format
 msgid ":math:`y_{1}= \\dfrac{y_{0}}{\\max\\left(y_{0}\\right)}`"
 msgstr ""
 
@@ -157,9 +216,6 @@ msgstr "Génère de nouveaux signaux en ajoutant le même bruit à chaque signal
 msgid "Noise"
 msgstr "Bruit"
 
-msgid "Description"
-msgstr "Description"
-
 msgid "Gaussian"
 msgstr "Gaussien"
 
@@ -786,9 +842,3 @@ msgstr "Dérivée de la déviation d'Allan, quantifie la stabilité en termes de
 
 msgid "The \"All stability features\" option allows to compute all stability analysis methods at once."
 msgstr "L'option \"Toutes les analyses de stabilité\" permet de calculer toutes les méthodes d'analyse de stabilité en une seule fois."
-
-msgid "X-Y Mode"
-msgstr "Mode XY"
-
-msgid "Simulate the X-Y mode of an oscilloscope."
-msgstr "Simuler le mode XY d'un oscilloscope."
diff --git a/doc/locale/fr/LC_MESSAGES/intro/keyfeatures.po b/doc/locale/fr/LC_MESSAGES/intro/keyfeatures.po
@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: DataLab \n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2025-09-10 10:01+0200\n"
+"POT-Creation-Date: 2025-12-03 11:35+0100\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -140,6 +140,12 @@ msgstr "Normalisation, rognage, correction de décalage"
 msgid "Reverse X-axis"
 msgstr "Inversion de l'axe X"
 
+msgid "Replace X by other signal's Y (calibration)"
+msgstr "Remplacer X par le Y d'un autre signal (calibration)"
+
+msgid "X-Y mode"
+msgstr "Mode X-Y"
+
 msgid "Thresholding (manual, Otsu...)"
 msgstr "Seuillage (manuel, Otsu...)"
 
@@ -158,9 +164,6 @@ msgstr "Interpolation, rééchantillonnage"
 msgid "Detrending"
 msgstr "Elimination de tendance"
 
-msgid "X-Y mode"
-msgstr "Mode XY"
-
 msgid "Interactive fit: Gauss, Lorentz, Voigt, polynomial, CDF..."
 msgstr "Ajustement interactif : Gauss, Lorentz, Voigt, polynôme, CDF..."
 
