feat: update reference handling in CIF tree and add d-spacing conversion functions

Author: fgjorup

plaid/misc.py

@@ -10,21 +10,43 @@
 """
 import numpy as np
 
+HC = 12.3984193  # Planck constant times speed of light in keV·Å
 
 def q_to_tth(q, E):
     """Convert q to 2theta."""
     # Convert 2theta to radians
-    wavelength = 12.398 / E
+    wavelength = HC / E
     tth = 2 * np.degrees(np.arcsin(q * wavelength / (4 * np.pi)))
     return tth
 
 def tth_to_q(tth, E):
     """Convert 2theta to q."""
     # Convert 2theta to radians
-    wavelength = 12.398 / E
+    wavelength = HC / E
     q = (4 * np.pi / wavelength) * np.sin(np.radians(tth) / 2)
     return q
 
+def d_to_q(d):
+    """Convert d-spacing to q."""
+    return 2 * np.pi / d
+
+def q_to_d(q):
+    """Convert q to d-spacing."""
+    return 2 * np.pi / q
+
+def d_to_tth(d, E):
+    """Convert d-spacing to 2theta."""
+    wavelength = HC / E
+    tth = 2 * np.degrees(np.arcsin(wavelength / (2 * d)))
+    return tth
+
+def tth_to_d(tth, E):
+    """Convert 2theta to d-spacing."""
+    wavelength = HC / E
+    d = wavelength / (2 * np.sin(np.radians(tth) / 2))
+    return d
+
+
 def get_divisors(x):
     """Get all divisors of an integer x."""
     divisors = []

plaid/plaid.py

@@ -37,7 +37,7 @@
 from plaid.dialogs import H5Dialog, ExportSettingsDialog, ColorCycleDialog
 from plaid.reference import Reference
 from plaid.plot_widgets import HeatmapWidget, PatternWidget, AuxiliaryPlotWidget, CorrelationMapWidget, DiffractionMapWidget
-from plaid.misc import q_to_tth, tth_to_q, get_divisors
+from plaid.misc import q_to_tth, tth_to_q, d_to_q, d_to_tth, get_divisors
 from plaid.data_containers import AzintData, AuxData
 from plaid import __version__ as CURRENT_VERSION
 import plaid.resources
@@ -168,7 +168,7 @@ def save_recent_refs_settings(recent_refs):
     recent_refs = [r for r in recent_refs if r]  # Remove empty entries
     # Limit to the last 10 references
     if len(recent_refs) > 10:
-        recent_refs = recent_refs[-10:]
+        recent_refs = recent_refs[:10]
     # Save the recent references
     settings.setValue("recent-references", recent_refs)
     settings.endGroup()
@@ -231,7 +231,7 @@ def __init__(self):
         self.E = None  # Energy in keV
         self.is_Q = False # flag to indicate if the data is in Q space (True) or 2theta space (False)
 
-        self.azint_data = AzintData()
+        self.azint_data = AzintData(self)
         self.aux_data = {}
 
         self.locked_patterns = []  # list of (is_Q, E) tuples for locked patterns
@@ -398,10 +398,11 @@ def _init_connections(self):
         self.file_tree.sigI0DataRequested.connect(self.load_I0_data)
         self.file_tree.sigAuxiliaryDataRequested.connect(self.load_auxiliary_data)
         # Connect the CIF tree signals to the appropriate slots
-        self.cif_tree.sigItemAdded.connect(self.add_reference)
-        self.cif_tree.sigItemChecked.connect(self.toggle_reference)
-        self.cif_tree.sigItemDoubleClicked.connect(self.rescale_reference)
-        self.cif_tree.sigItemRemoved.connect(self.remove_reference)
+        self.cif_tree.sigItemAdded.connect(self.add_reference)              # --> str
+        self.cif_tree.sigItemChecked.connect(self.toggle_reference)         # --> int, bool
+        self.cif_tree.sigItemDoubleClicked.connect(self.rescale_reference)  # --> int, str
+        self.cif_tree.sigItemRemoved.connect(self.remove_reference)         # --> int
+        self.cif_tree.sigItemReloadRequested.connect(self.reload_reference) # --> int
         # Connect the heatmap signals to the appropriate slots
         self.heatmap.sigHLineMoved.connect(self.hline_moved)
         self.heatmap.sigXRangeChanged.connect(self.pattern.set_xrange)
@@ -1008,24 +1009,49 @@ def add_reference(self, cif_file, Qmax=None):
         self.plot_reference(color=color)
         tooltip = f"{self.ref.get_spacegroup_info()}\n{self.ref.get_cell_parameter_info()}"
         self.cif_tree.set_latest_item_tooltip(tooltip)
-
-    def plot_reference(self, Qmax=None, dmin=None, color=None):
-        """Plot the reference pattern in the pattern plot."""
+        
+    def get_reference_reflections(self, Qmax=None, dmin=None):
+        """
+        Get the reference reflections from the current reference pattern,
+        converted to the current x-axis units.
+        """
         if Qmax is None:
             Qmax = self.getQmax()
         hkl, d, I = self.ref.get_reflections(Qmax=Qmax, dmin=dmin)
         if len(hkl) == 0:
             QMessageBox.warning(self, "No Reflections", "No reflections found in the reference pattern.")
             return
-        
         if self.is_Q:
             # Convert d to Q
-            x = 4*np.pi/d
+            x = d_to_q(d)
         else:
             # Convert d to 2theta
-            x = np.degrees(2 * np.arcsin((12.398 / self.E) / (2 * d)))
+            x = d_to_tth(d, self.E)
+        return hkl, x, I
+
+    def plot_reference(self, Qmax=None, dmin=None, color=None):
+        """Plot the reference pattern in the pattern plot."""
+        hkl, x, I = self.get_reference_reflections(Qmax=Qmax, dmin=dmin)
         self.pattern.add_reference(hkl, x, I,color=color)
 
+    def reload_reference(self,index, Qmax=None):
+        """Reload the reference pattern at the given index from the cif tree."""
+        cif_file = self.cif_tree.files[index]
+        # check that the cif file still exists
+        if not os.path.exists(cif_file):
+            QMessageBox.critical(self, "Error", f"CIF file not found: {cif_file}")
+            return
+        item = self.cif_tree.file_tree.topLevelItem(index)
+        if Qmax is None:
+            Qmax = self.getQmax()
+        self.ref = Reference(cif_file,E=self.E, Qmax=Qmax)
+        hkl, x, I = self.get_reference_reflections(Qmax=Qmax)
+        self.pattern.update_reference(index, hkl, x, I)
+        # update the tooltip
+        tooltip = f"{self.ref.get_spacegroup_info()}\n{self.ref.get_cell_parameter_info()}"
+        item.setToolTip(0, tooltip)
+        self.statusBar().showMessage(f"Reloaded reference from {cif_file}")
+
     def toggle_reference(self, index, is_checked):
         """
         Toggle the visibility of the reference pattern.
@@ -1039,6 +1065,7 @@ def rescale_reference(self,index,name):
         This method is called when a reference item is double-clicked in the CIF tree.
         """
         self.pattern.rescale_reference(index)
+        self.statusBar().showMessage(f"Rescaled {name}")
 
     def load_I0_data(self, aname=None, fname=None):
         """Load auxillary data as I0. Called when the user requests I0 data from the file tree."""

plaid/plot_widgets.py

@@ -678,7 +678,6 @@ def remove_locked_pattern(self):
         pattern = self.locked_pattern_items.pop(-1)
         self.plot_widget.getPlotItem().removeItem(pattern)
         self.legend.removeItem(pattern)
-        
 
     def add_reference(self, hkl, x, I,color=None):
         """Add a reference pattern to the plot."""
@@ -692,15 +691,24 @@ def add_reference(self, hkl, x, I,color=None):
         self.plot_widget.getPlotItem().addItem(reference_item)
         self.reference_items.append(reference_item)
         self.reference_hkl[reference_item] = (x,hkl)  # Store the hkl indices for the reference item
-        # tth = np.degrees(np.arcsin(lambd/(2*d)))*2
+        self._set_reference_data(reference_item, x, I)
+
+    def update_reference(self, index, hkl, x, I):
+        """Update a reference pattern in the plot."""
+        reference_item = self.reference_items[index]
+        self.reference_hkl[reference_item] = (x,hkl)  # Update the hkl indices for the reference item
+        self._set_reference_data(reference_item, x, I)
+
+    def _set_reference_data(self, item, x, I):
+        """Set the data for a reference pattern item."""
         x = np.repeat(x,2)
         I = np.repeat(I,2)
         I[::2] = 0  # Set the intensity to 0 for the first point of each pair
         if self.y is None:
             scale = 100
         else:
             scale = self.y.max() if self.y.max()>0 else 1.
-        reference_item.setData(x, I*scale)  # Initialize with test data
+        item.setData(x, I*scale)  # Update with new data
 
     def remove_reference(self, index=-1):
         """Remove a reference pattern from the plot."""

plaid/trees.py

@@ -331,6 +331,7 @@ class CIFTreeWidget(QWidget):
     sigItemChecked = QtCore.pyqtSignal(int, bool)
     sigItemDoubleClicked = QtCore.pyqtSignal(int, str)
     sigItemRemoved = QtCore.pyqtSignal(int)
+    sigItemReloadRequested = QtCore.pyqtSignal(int)
     def __init__(self, parent=None):
         super().__init__(parent)
         self.parent = parent
@@ -433,13 +434,13 @@ def customMenuEvent(self, pos):
         # create a context menu for the item
         menu = QMenu(self)
         # # add an action to reload the CIF file
-        # reload_action = menu.addAction("Reload CIF")
-        # reload_action.setToolTip("Reload the selected CIF file")
-        # reload_action.triggered.connect(lambda: print("reload action triggered"))  # Placeholder for reload action
+        reload_action = menu.addAction("Reload CIF")
+        reload_action.setToolTip("Reload the selected CIF file")
+        reload_action.triggered.connect(lambda: self._request_reload(item))
         # add an action to remove the item
         remove_action = menu.addAction("Remove")
         remove_action.setToolTip("Remove the selected CIF file from the tree")
-        remove_action.triggered.connect(lambda: self.remove_item(item))  # Placeholder for remove action
+        remove_action.triggered.connect(lambda: self.remove_item(item))
         menu.exec(self.file_tree.viewport().mapToGlobal(pos))
         menu.deleteLater()  # Clean up the menu after use
 
@@ -469,6 +470,12 @@ def _update_item_colors(self):
             color = QColor(self.color_cycle[i % len(self.color_cycle)])
             item.setForeground(0, color)
 
+    def _request_reload(self, item):
+        """Request reload of the specified item. Emits the sigItemReloadRequested signal with the index of the item."""
+        index = self.file_tree.indexOfTopLevelItem(item)
+        if index == -1:
+            return
+        self.sigItemReloadRequested.emit(index)
 
 if __name__ == "__main__":
     pass