more changes for interactions with current EDL/ES

Projects load Examples load Properties change Profile gets calculated Charts get generated and updated - Fitting doesn't work
EasyScience · Oct 7, 2024 · 8560760 · 8560760
1 parent 5a06e13
commit 8560760
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Showing 11 changed files with 1,792 additions and 1,749 deletions.
diff --git a/easyDiffractionApp/Gui/Components/Pages/Model/SideBarText/Models.qml b/easyDiffractionApp/Gui/Components/Pages/Model/SideBarText/Models.qml
@@ -64,7 +64,8 @@ EaElements.ComboBox {
 
                 EaComponents.TableViewParameter {
                     enabled: false
-                    text: comboBox.model[index].name
+                    // text: comboBox.model[index].name
+                    text: "none"
                 }
             }
         }

diff --git a/easyDiffractionApp/Logic/Experiment.py b/easyDiffractionApp/Logic/Experiment.py
@@ -260,7 +260,7 @@ def jobToBlock(self, job=None):
         cifDict = 'core'
         dataBlock = {'name': '', 'params': {}, 'loops': {}}
         dataBlock['name'] = dict(Parameter(
-            value = job.name,
+            value = job.experiment.name,
             icon = 'microscope'))
         param = 'params'
         category = '_diffrn_radiation'
@@ -680,7 +680,8 @@ def replaceExperiment(self, edCifNoMeas=''):
         currentDataBlock = self._dataBlocksNoMeas[self.currentIndex]
         currentExperimentName = currentDataBlock['name']['value']
 
-        calcObjBlockNames = [item.data_name for item in self._interface.data()._calcObj]
+        # calcObjBlockNames = [item.data_name for item in self._interface.data()._calcObj]
+        calcObjBlockNames = [item.data_name for item in self._interface.data()._cryspyObj]
         calcObjBlockIdx = calcObjBlockNames.index(currentExperimentName)
 
         if not edCifNoMeas:
@@ -811,7 +812,9 @@ def appendDataBlockLoopRow(self, category):
         lastBkgPoint = self._dataBlocksNoMeas[blockIdx]['loops'][category][-1]
 
         newBkgPoint = copy.deepcopy(lastBkgPoint)
-        newBkgPoint['line_segment_X']['value'] += 10
+        point = float(newBkgPoint['line_segment_X']['value'])
+        newBkgPoint['line_segment_X']['value'] = point + 10
+        # newBkgPoint['line_segment_X']['value'] += 10
 
         self._dataBlocksNoMeas[blockIdx]['loops'][category].append(newBkgPoint)
         atomsCount = len(self._dataBlocksNoMeas[blockIdx]['loops'][category])
@@ -891,7 +894,8 @@ def blocksToLoopJob(self, blockIdx, category, name, rowIndex, field, value):
         p_category = BLOCK2JOB[category]
         # get category
         # assumption of the first loop, since there is only one background currently
-        job_with_category = getattr(self.job, p_category)[0]
+        # job_with_category = getattr(self.job, p_category)[0]
+        job_with_category = getattr(self.job, p_category)
         # should we get the loop item?
         # this works for the background, but not for scale etc.
         try:
@@ -1190,21 +1194,20 @@ def isSpinPolarized(self):
     def runProfileCalculations(self):
 
         # shove it all into the calculator.
-
         result = self._interface.calculate_profile()
-        # debug stuff - remove before merging
-        # simx = self._xArrays
-        # simx = self._dataBlocksMeasOnly[0]['loops']['_pd_meas'][0]['2theta_scan']['value']
-        # result = self._job.create_simulation(simx)
-
         console.debug(formatMsg('sub', 'Profle calculations', 'finished'))
 
         chiSq = result[0]
-        self._proxy.fitting._pointsCount = result[1]
-        self._proxy.fitting._freeParamsCount = len(result[4])
-        self._proxy.fitting.chiSq = chiSq / (self._proxy.fitting._pointsCount - self._proxy.fitting._freeParamsCount)
+        chiSqn = chiSq / (result[1] - len(result[4]))
+        self._proxy.status.goodnessOfFit = f'{chiSqn:0.2f}'
+
+        # code left to reuse the format statements later
+        #################################################
+        # self._proxy.fitting._pointsCount = result[1]
+        # self._proxy.fitting._freeParamsCount = len(result[4])
+        # self._proxy.fitting.chiSq = chiSq / (self._proxy.fitting._pointsCount - self._proxy.fitting._freeParamsCount)
 
-        gofLastIter = self._proxy.fitting.chiSq  # NEED FIX
+        # gofLastIter = self._proxy.fitting.chiSq  # NEED FIX
         # if self._proxy.fitting.chiSqStart is None:
         #     self._proxy.status.goodnessOfFit = f'{gofLastIter:0.2f}'                           # NEED move to connection
         # else:

diff --git a/easyDiffractionApp/Logic/Fittables.py b/easyDiffractionApp/Logic/Fittables.py
@@ -64,7 +64,7 @@ def resetAll(self):
     def data(self):
         #console.error('FITTABLES DATA GETTER')
         return self._data
-
+    
     @Property(str, notify=dataJsonChanged)
     def dataJson(self):
         return self._dataJson

diff --git a/easyDiffractionApp/Logic/Fitting.py b/easyDiffractionApp/Logic/Fitting.py
@@ -10,7 +10,7 @@
 from PySide6.QtCore import QObject, Signal, Slot, Property, QThreadPool
 
 from EasyApp.Logic.Logging import console
-from easydiffraction.io.helpers import formatMsg
+from easydiffraction.io.Helpers import formatMsg
 from Logic.Data import Data
 
 try:

diff --git a/easyDiffractionApp/Logic/Fitting2.py b/easyDiffractionApp/Logic/Fitting2.py
@@ -48,6 +48,7 @@ def __init__(self, proxy=None, interface=None):
         self._job = self.parent.job
         # self.fitter = CoreFitter(self.parent.sample(), self.interface.fit_func)
         self.fitter = CoreFitter(self._job, self._job.calculate_profile)
+        # self.fitter = CoreFitter(self._job, self._job.interface.calculate_profile)
         # self.fitter = CoreFitter(self.parent.experiment.job(), self.interface.fit_func)
 
         # Multithreading
@@ -91,6 +92,9 @@ def fit_nonpolar(self):
         try:
             res = self.fitter.fit(x, y, **kwargs)
 
+            #self._job.fit(**kwargs)
+            # res = self._job.fitting_results
+
         except Exception as ex:
             self.failed.emit(str(ex))
             return

diff --git a/easyDiffractionApp/Logic/Model.py b/easyDiffractionApp/Logic/Model.py
@@ -50,7 +50,7 @@
 
 BLOCK2PHASE = {
     '_cell': 'cell',
-    '_space_group': 'spacegroup',
+    '_space_group': 'space_group',
     '_atom_site': 'atoms',
     'occupancy': 'occupancy',
     'fract_x': 'fract_x',
@@ -66,6 +66,7 @@
     'crystal_system': 'crystal_system',
     'IT_number': 'int_number',
     'IT_coordinate_system_code': 'setting',
+    'B_iso_or_equiv': 'Biso',
 }
 class Model(QObject):
     definedChanged = Signal()
@@ -197,7 +198,7 @@ def atomData(self, typeSymbol, key):
     def addDefaultModel(self):
         console.debug("Adding default model(s)")
         self.loadModelsFromEdCif(_DEFAULT_CIF_BLOCK)
-        self.addDefaultPhase()
+        # self.addDefaultPhase()
 
     @Slot('QVariant')
     def loadModelsFromResources(self, fpaths):
@@ -228,27 +229,31 @@ def loadModelsFromFiles(self, fpaths):
     # @Slot(str)
     def loadModelsFromEdCif(self, edCif):
         # Update the Phases object
-        phases = Phases.from_cif_string(edCif)
-        phases.interface = self._interface
-        for phase in phases:
-            phase.scale.fixed = True
-            # self.phases.append(phase)
-            self.job.add_phase(phase=phase)
+        self.job.add_sample_from_string(edCif)
+
+        # phases = Phases.from_cif_string(edCif)
+        # phases.interface = self._interface
+        # for phase in phases:
+        #    phase.scale.fixed = True
+        #    # self.phases.append(phase)
+        #    self.job.add_phase(phase=phase)
+
         self._currentIndex = len(self.job.phases) - 1
         # convert phase into dataBlocks
         dataBlocks = self.phaseToBlocks(self.job.phases)
         self._dataBlocks.append(dataBlocks)
         self.defined = bool(len(self._dataBlocks))
 
         self.setDataBlocksCif()
-        self.updateCifOnInterface()
+        self.updateCifOnInterface(cif=edCif)
         self.dataBlocksChanged.emit()
 
-    def updateCifOnInterface(self):
+    def updateCifOnInterface(self, cif=None):
         '''
         Update the CIF representation on the current interface
         '''
-        cif = self._dataBlocksCif[self.currentIndex][0]
+        if cif is None:
+            cif = self._dataBlocksCif[self.currentIndex][0]
         self._interface.updateModelCif(cif)
 
     def phaseToBlocks(self, phases):
@@ -483,6 +488,8 @@ def blocksToLoopPhase(self, blockIdx, category, name, rowIndex, field, value):
         p_category = BLOCK2PHASE[category]
         # get category
         phase_with_category = getattr(phase, p_category)[rowIndex]
+        if p_name == 'Biso':
+            phase_with_category = getattr(phase_with_category, 'adp')
         # get loop item
         phase_with_item = getattr(phase_with_category, p_name)
         if field == 'value':
@@ -691,10 +698,10 @@ def editCalculatorDictByMainParam(self, blockIdx, category, name, field, value):
         if field == 'fit':
             path[1] = f'flags_{path[1]}'
 
-        oldValue = self._interface.data()._cryspyDict[path[0]][path[1]][path[2]]
+        oldValue = self._interface.data()._cryspyDict[path[0].lower()][path[1]][path[2]]
         if oldValue == value:
             return False
-        self._interface.data()._cryspyDict[path[0]][path[1]][path[2]] = value
+        self._interface.data()._cryspyDict[path[0].lower()][path[1]][path[2]] = value
 
         console.debug(formatMsg('sub', 'Calculator dict', f'{oldValue} → {value}', f'{path}'))
         return True

diff --git a/easyDiffractionApp/Logic/Plotting.py b/easyDiffractionApp/Logic/Plotting.py
@@ -91,7 +91,7 @@ def setQtChartsSerieRef(self, page, serie, ref):
         #if self._chartRefs['QtCharts'][page][serie] == ref:
         #    return
         if ref.name():  # braggSeries
-            self._chartRefs['QtCharts'][page][serie][ref.name()] = ref
+            self._chartRefs['QtCharts'][page][serie][ref.name().lower()] = ref
             console.debug(formatMsg('sub', f'{serie} with name {ref.name()} on {page}: {ref}'))
         else:  # other series
             self._chartRefs['QtCharts'][page][serie] = ref

diff --git a/easyDiffractionApp/Logic/PyProxy.py b/easyDiffractionApp/Logic/PyProxy.py
@@ -24,10 +24,11 @@
 class PyProxy(QObject):
     def __init__(self, parent=None):
         super().__init__(parent)
+        # self.interface = InterfaceFactory()
         # instantiate the Job object.
         # This is done only once, since in the App world there is only one Job
         self._job = Job()
-        self.interface = InterfaceFactory()
+        self.interface = self._job.interface
         self._logger = LoggerLevelHandler(self)
         self._project = Project(self)
         self._experiment = Experiment(self, interface=self.interface)

diff --git a/easyDiffractionApp/Logic/Tables.py b/easyDiffractionApp/Logic/Tables.py
@@ -97,6 +97,23 @@
     "U": "#D0D0E0",
     "Np": "#D0D0E0",
     "Pu": "#D0D0E0",
+    "Am": "#D0D0E0",
+    "Cm": "#D0D0E0",
+    "Bk": "#D0D0E0",
+    "Cf": "#D0D0E0",
+    "Es": "#D0D0E0",
+    "Fm": "#D0D0E0",
+    "Md": "#D0D0E0",
+    "No": "#D0D0E0",
+    "Lr": "#D0D0E0",
+    "Rf": "#D0D0E0",
+    "Db": "#D0D0E0",
+    "Sg": "#D0D0E0",
+    "Bh": "#D0D0E0",
+    "Hs": "#D0D0E0",
+    "Mt": "#D0D0E0",
+    "Ds": "#D0D0E0",
+    "Rg": "#D0D0E0",
 }
 PERIODIC_TABLE = {
     "H": {