Tabs, Batch Processing and 2D data slicing and processing for pr

build_tools/release_notes/6.0.0_notes.txt

@@ -27,7 +27,7 @@
 
 ## Anticipated for beta version
 - PDB-based model saved to custom model (for S(q) calculations)?
-- Batch Processing and 2D data slicing and processing for P(r)
+- Batch Processing for P(r)
 - Local documentation generator
 - Log explorer
 - Send To button with replacement options

src/sas/qtgui/MainWindow/DataExplorer.py

@@ -616,8 +616,22 @@ def updatePerspectiveWithProperties(self, key, value):
         if 'pr_params' in value:
             self.cbFitting.setCurrentIndex(self.cbFitting.findText('Inversion'))
             params = value['pr_params']
-            self.sendItemToPerspective(items[0])
-            self._perspective().updateFromParameters(params)
+            # Make the perspective read the rest of the read data
+            if not isinstance(params, list):
+                params = [params]
+            for page in params:
+            # Check if this set of parameters is for a batch page
+                            # if so, skip the update
+                if page['is_batch'][0] == 'True':
+                    continue
+                tab_index = None
+                if 'tab_index' in page:
+                    tab_index = page['tab_index'][0]
+                    tab_index = int(tab_index)
+                # Send current model item to the perspective
+                self.sendItemToPerspective(items[0], tab_index=tab_index)
+                # Assign parameters to the most recent (current) page. 
+                self._perspective().updateFromParameters(page)
         if 'invar_params' in value:
             self.cbFitting.setCurrentIndex(self.cbFitting.findText('Invariant'))
             self.sendItemToPerspective(items[0])

src/sas/qtgui/MainWindow/UnitTesting/GuiManagerTest.py

@@ -32,9 +32,9 @@ def manager(self, qapp):
         '''Create/Destroy the GUI Manager'''
         class MainWindow(MainSasViewWindow):
             # Main window of the application
-            def __init__(self, reactor, parent=None):
-                screen_resolution = QtCore.QRect(0,0,640,480)
-                super(MainWindow, self).__init__(screen_resolution, parent)
+
+            def __init__(self,  parent=None):
+                super(MainWindow, self).__init__( parent)
 
                 # define workspace for dialogs.
                 self.workspace = QMdiArea(self)

src/sas/qtgui/Perspectives/Corfunc/CorfuncPerspective.py

@@ -468,6 +468,9 @@ def setData(self, data_item: List[QStandardItem], is_batch=False):
         model_item = data_item[0]
         data = GuiUtils.dataFromItem(model_item)
         self.data = data
+        if not isinstance(self.data, Data1D):
+            msg = "Invariant cannot be computed with 2D data."
+            raise ValueError(msg)
         self._model_item = model_item
 
         self.model.itemChanged.disconnect(self.model_changed)

src/sas/qtgui/Perspectives/Corfunc/CorfuncSlider.py

@@ -217,13 +217,14 @@ def extrapolation_parameters(self):
         return ExtrapolationParameters(self._min, self._point_1, self._point_2, self._point_3, self._max)
 
     @extrapolation_parameters.setter
-    def extrapolation_parameters(self, params: ExtrapolationParameters):
-        if self.find_parameter_problems(params) is None:
-            self._min = params.data_q_min
-            self._point_1 = params.point_1
-            self._point_2 = params.point_2
-            self._point_3 = params.point_3
-            self._max = params.data_q_max
+    def extrapolation_parameters(self, params: Optional[ExtrapolationParameters]):
+        if params is not None:
+            if self.find_parameter_problems(params) is None:
+                self._min = params.data_q_min
+                self._point_1 = params.point_1
+                self._point_2 = params.point_2
+                self._point_3 = params.point_3
+                self._max = params.data_q_max
 
         self.update()
 

src/sas/qtgui/Perspectives/Inversion/DMaxExplorerWidget.py

@@ -150,8 +150,11 @@ def modelChanged(self, item):
                 plotable_xs.append(x)
             except Exception as ex:
                 # This inversion failed, skip this D_max value
-                msg = "ExploreDialog: inversion failed "
-                msg += "for D_max=%s\n%s" % (str(x), ex)
+
+                msg = (f"ExploreDialog: inversion failed for D_max={x}\n"
+                       f"{ex}\n"
+                       f"Please adapt Inversion parameters")
+
                 logger.error(msg)
 
         #Return the invertor to its original state

src/sas/qtgui/Perspectives/Inversion/InversionLogic.py

@@ -2,7 +2,7 @@
 import logging
 import numpy as np
 
-from sas.qtgui.Plotting.PlotterData import Data1D
+from sas.qtgui.Plotting.PlotterData import Data1D, Data2D
 
 PR_FIT_LABEL = r"$P_{fit}(r)$"
 PR_LOADED_LABEL = r"$P_{loaded}(r)$"
@@ -27,6 +27,8 @@ def __init__(self, data=None):
         self.data_is_loaded = False
         if data is not None:
             self.data_is_loaded = True
+        self.qmin = 0.0    
+        self.qmax = np.inf    
 
     @property
     def data(self):
@@ -42,7 +44,7 @@ def isLoadedData(self):
         """ accessor """
         return self.data_is_loaded
 
-    def new1DPlot(self, out, pr, q=None):
+    def new1DPlot(self, tab_id=1, out=None, pr=None, q=None):
         """
         Create a new 1D data instance based on fitting results
         """
@@ -72,7 +74,9 @@ def new1DPlot(self, out, pr, q=None):
             logger.info("Could not compute I(q) for q =", list((x[index])))
 
         new_plot = Data1D(x, y)
-        new_plot.name = IQ_FIT_LABEL + f"[{self._data.name}]"
+        new_plot.is_data = False
+        new_plot.dy = np.zeros(len(y))
+        new_plot.name = "%s [%s]" % (IQ_FIT_LABEL, self._data.name)
         new_plot.xaxis("\\rm{Q}", 'A^{-1}')
         new_plot.yaxis("\\rm{Intensity} ", "cm^{-1}")
         title = "I(q)"
@@ -81,7 +85,7 @@ def new1DPlot(self, out, pr, q=None):
         # If we have a group ID, use it
         if 'plot_group_id' in pr.info:
             new_plot.group_id = pr.info["plot_group_id"]
-        new_plot.id = IQ_FIT_LABEL
+        new_plot.id = str(tab_id) +IQ_FIT_LABEL
 
 
         # If we have used slit smearing, plot the smeared I(q) too
@@ -111,6 +115,8 @@ def new1DPlot(self, out, pr, q=None):
 
         return new_plot
 
+
+
     def newPRPlot(self, out, pr, cov=None):
         """
         """
@@ -124,7 +130,7 @@ def newPRPlot(self, out, pr, cov=None):
             (y, dy) = pr.pr_err(out, cov, x)
             new_plot = Data1D(x, y, dy=dy)
 
-        new_plot.name = PR_FIT_LABEL + f"[{self._data.name}]"
+        new_plot.name = "%s [%s]" % (PR_FIT_LABEL, self._data.name)
         new_plot.xaxis("\\rm{r}", 'A')
         new_plot.yaxis("\\rm{P(r)} ", "cm^{-3}")
         new_plot.title = "P(r) fit"
@@ -135,12 +141,18 @@ def newPRPlot(self, out, pr, cov=None):
 
         return new_plot
 
-    def add_errors(self, sigma=0.05):
+    def add_errors(self, sigma=1.0):
         """
         Adds errors to data set is they are not available.
         Uses  $\Delta y = \sigma | y |$.
         """
-        self._data.dy = sigma * np.fabs(self._data.y)
+        if self.data.dy.size == 0.0:
+            self.data.dy = np.sqrt(np.fabs(self.data.y))*sigma
+
+        if self.data.dy is not None:
+            self.data.dy = np.where(self.data.dy < 0.0, np.sqrt(np.fabs(self.data.y))*sigma, self.data.dy)
+            self.data.dy = np.where(np.fabs(self.data.dy) < 1e-16, 1e16, self.data.dy)
+        return self.data.dy
 
     def computeDataRange(self):
         """
@@ -156,8 +168,13 @@ def computeRangeFromData(self, data):
         qmin, qmax = None, None
         if isinstance(data, Data1D):
             try:
-                qmin = min(data.x)
                 qmax = max(data.x)
+                #set q values where Intensity is zero, 
+                #to qmax and exclude from minimum accepted q
+                #to avoid dodgy points around beam stop
+                usable_qrange=np.where(data.y <= 0, qmax, data.x)
+                qmin = min(usable_qrange)
+
             except (ValueError, TypeError):
                 msg = "Unable to find min/max/length of \n data named %s" % \
                             self.data.filename