enable debugging.

Add cif-read Phase object

easyDiffractionApp/Examples/PbSO4/models/pbso4.cif

@@ -1,8 +1,8 @@
 data_pbso4
 
-_cell.length_a 8.4693(1)
-_cell.length_b 5.3910(1)
-_cell.length_c 6.9506(1)
+_cell.length_a 8.4693
+_cell.length_b 5.3910
+_cell.length_c 6.9506
 _cell.angle_alpha 90
 _cell.angle_beta 90
 _cell.angle_gamma 90

easyDiffractionApp/Logic/Model.py

@@ -10,6 +10,9 @@
 from PySide6.QtCore import QFile, QTextStream, QIODevice
 from PySide6.QtQml import QJSValue
 
+from easyDiffractionLib import Phases, Phase, Lattice, Site, SpaceGroup
+from easyCrystallography.Components.AtomicDisplacement import AtomicDisplacement
+
 from EasyApp.Logic.Logging import console
 from Logic.Helpers import IO
 from Logic.Calculators import CryspyParser
@@ -84,6 +87,8 @@ def __init__(self, parent):
         self._spaceGroupNames = self.createSpaceGroupNames()
         self._isotopesNames = self.createIsotopesNames()
 
+        self.phases = Phases()
+
     # QML accessible properties
 
     @Property('QVariant', constant=True)
@@ -139,6 +144,27 @@ def structViewCellModel(self):
     def structViewAxesModel(self):
         return self._structViewAxesModel
 
+    def addDefaultPhase(self):
+        default_phase = self._defaultPhase()
+        r = re.compile('(.+[^0-9])\d*$')
+        known_phases = [r.findall(s)[0] for s in self.phases.phase_names]  # Strip out any 1, 2, 3 etc we may have added
+        if default_phase.name in known_phases:
+            idx = known_phases.count(default_phase.name)
+            default_phase.name = default_phase.name + str(idx)
+        # print('Disabling scale')
+        default_phase.scale.fixed = True
+        self.phases.append(default_phase)
+
+    # @staticmethod
+    def _defaultPhase(self):
+        space_group = SpaceGroup('F d -3:2')
+        cell = Lattice(5.0, 3.0, 4.0, 90, 90, 90)
+        adp = AtomicDisplacement("Uiso")
+        atom = Site(label='O', specie='O', fract_x=0.0, fract_y=0.0, fract_z=0.0, adp=adp)#, interface=self._interface)
+        phase = Phase('Test', spacegroup=space_group, cell=cell)#, interface=self._interface)
+        phase.add_atom(atom)
+        return phase
+
     # QML accessible methods
 
     @Slot(str, str, result=str)
@@ -152,6 +178,7 @@ def atomData(self, typeSymbol, key):
     def addDefaultModel(self):
         console.debug("Adding default model(s)")
         self.loadModelsFromEdCif(_DEFAULT_CIF_BLOCK)
+        self.addDefaultPhase()
 
     @Slot('QVariant')
     def loadModelsFromResources(self, fpaths):
@@ -179,6 +206,9 @@ def loadModelsFromFiles(self, fpaths):
                 edCif = file.read()
             self.loadModelsFromEdCif(edCif)
 
+            phase = Phases.from_cif_file(fpath)
+            self.phases.append(phase)
+
     @Slot(str)
     def loadModelsFromEdCif(self, edCif):
         cryspyObj = self._proxy.data._cryspyObj
@@ -311,6 +341,7 @@ def duplicateLoopRow(self, category, idx):
     # Private methods
 
     def cryspyObjCrystals(self):
+        print("\ncryspyObjCrystals\n")
         cryspyObj = self._proxy.data._cryspyObj
         cryspyModelType = cryspy.E_data_classes.cl_1_crystal.Crystal
         models = [block for block in cryspyObj.items if type(block) == cryspyModelType]
@@ -333,6 +364,7 @@ def removeDataBlockLoopRow(self, category, rowIndex):
         console.debug(IO.formatMsg('sub', 'Intern dict', 'removed', f'{block}[{blockIdx}].{category}[{rowIndex}]'))
 
     def appendDataBlockLoopRow(self, category):
+        print("\nappendDataBlockLoopRow\n")
         block = 'model'
         blockIdx = self._currentIndex
 
@@ -658,11 +690,14 @@ def setCurrentModelStructViewAxesModel(self):
         self.structViewAxesModelChanged.emit()
 
     def setCurrentModelStructViewAtomsModel(self):
+        print("\nsetCurrentModelStructViewAtomsModel\n")
         structViewModel = set()
         currentModelIndex = self._proxy.model.currentIndex
         models = self.cryspyObjCrystals()
         spaceGroup = [sg for sg in models[currentModelIndex].items if type(sg) == cryspy.C_item_loop_classes.cl_2_space_group.SpaceGroup][0]
         atoms = self._dataBlocks[self._currentIndex]['loops']['_atom_site']
+
+
         # Add all atoms in the cell, including those in equivalent positions
         for atom in atoms:
             symbol = atom['type_symbol']['value']

easyDiffractionApp/main.py

@@ -64,16 +64,22 @@
     engine.load(resourcePaths.splashScreenQml)
     console.debug('Splash screen QML component loaded')
 
+    from Logic.PyProxy import PyProxy
+    pyproxy = PyProxy()
+    engine.rootContext().setContextProperty('pyProxy', pyproxy)
+
     if not engine.rootObjects():
         sys.exit(-1)
     console.debug('QML engine has root component')
 
-    from Logic.Helpers import PyProxyWorker
-    from PySide6.QtCore import QThreadPool
-    worker = PyProxyWorker(engine)
-    worker.pyProxyExposedToQml.connect(lambda: engine.load(resourcePaths.mainQml))
-    threadpool = QThreadPool.globalInstance()
-    threadpool.start(worker.exposePyProxyToQml)
+    #from Logic.Helpers import PyProxyWorker
+    #from PySide6.QtCore import QThreadPool
+    #worker = PyProxyWorker(engine)
+    #worker.pyProxyExposedToQml.connect(lambda: engine.load(resourcePaths.mainQml))
+    #threadpool = QThreadPool.globalInstance()
+    #threadpool.start(worker.exposePyProxyToQml)
+
+    engine.load(resourcePaths.mainQml)
     console.debug('PyProxy object is creating in a separate thread and exposing to QML')
 
     console.debug('Application event loop is about to start')