orGUI 1.0.1__py3-none-any.whl

orgui/app/__init__.py

@@ -0,0 +1,36 @@
+# -*- coding: utf-8 -*-
+# /*##########################################################################
+#
+# Copyright (c) 2020-2024 Timo Fuchs
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__author__ = "Timo Fuchs"
+__copyright__ = "Copyright 2020-2024 Timo Fuchs"
+__license__ = "MIT License"
+__version__ = "1.0.0"
+__maintainer__ = "Timo Fuchs"
+__email__ = "fuchs@physik.uni-kiel.de"
+
+"""Module descripiton
+
+"""
+
+__all__ = ['orGUI','QReflectionSelector','QSpecScanSelector','QUBCalculator','database']

orgui/app/database.py

@@ -0,0 +1,487 @@
+# -*- coding: utf-8 -*-
+# /*##########################################################################
+#
+# Copyright (c) 2020-2024 Timo Fuchs
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__author__ = "Timo Fuchs"
+__copyright__ = "Copyright 2020-2024 Timo Fuchs"
+__license__ = "MIT License"
+__version__ = "1.0.0"
+__maintainer__ = "Timo Fuchs"
+__email__ = "fuchs@physik.uni-kiel.de"
+
+import sys
+import numpy as np
+import silx.gui.hdf5
+from silx.gui import icons
+from silx.gui.data import DataViewerFrame
+from silx.gui.hdf5.Hdf5TreeModel import Hdf5TreeModel
+from silx.gui.data import DataViewerFrame
+from silx.gui import qt
+import tempfile
+import silx.io.h5py_utils
+from silx.io import nxdata
+import silx.io.utils
+import h5py
+
+import datetime
+import os
+import traceback
+import time
+
+from ..datautils.xrayutils import unitcells
+from ..datautils.xrayutils import HKLVlieg, CTRcalc
+from ..datautils.xrayutils import DetectorCalibration
+
+from silx.io.dictdump import dicttonx ,nxtodict
+
+
+class ConfigData(qt.QObject):
+    def __init__(self, config=None):
+        self.detector = DetectorCalibration.Detector2D_SXRD()
+        
+        pass
+    
+    #@classmethod
+    def readConfig(self, filename):
+        config = configparser.ConfigParser()
+        config.read(configfile)
+        
+        machine = config['Machine']
+        lattice = config['Lattice']
+        diffrac = config['Diffractometer']
+            
+        self.azimuth = np.deg2rad(diffrac.getfloat('azimuthal_reference',0))
+        self.polaxis = np.deg2rad(diffrac.getfloat('polarization_axis',90))
+        self.polfactor = diffrac.getfloat('polarization_factor',0)
+            
+        sdd = machine.getfloat('SDD',0.729) #m
+        E =  machine.getfloat('E',78.0) #keV
+        pixelsize = machine.getfloat('pixelsize',172e-6) #m
+        cpx = machine.getfloat('cpx',731)
+        cpy = machine.getfloat('cpy',1587)
+        cp = [cpx,cpy]
+
+        self.mu = np.deg2rad(diffrac.getfloat('mu',0.05))
+        self.chi = np.deg2rad(diffrac.getfloat('chi',0.0))
+        self.phi = np.deg2rad(diffrac.getfloat('phi',0.0))
+            
+
+        a1 = lattice.getfloat('a1',-1)
+        a2 = lattice.getfloat('a2',-1)
+        a3 = lattice.getfloat('a3',-1)
+        alpha1 = lattice.getfloat('alpha1',-1)
+        alpha2 = lattice.getfloat('alpha2',-1)
+        alpha3 = lattice.getfloat('alpha3',-1)
+        self.n = 1 - lattice.getfloat('refractionindex',0.0)
+            
+        lat = np.array([a1,a2,a3])
+            
+        latticeoverride = True
+        latangle = np.array([alpha1,alpha2,alpha3])
+        if np.any(lat < 0.) or np.any(latangle < 0):
+            latticeoverride = False
+            a1 = a2 = a3 = 1.
+            alpha1 = alpha2 = alpha3 = 90.
+            
+        
+        self.crystal = CTRcalc.UnitCell([a1,a2,a3],[alpha1,alpha2,alpha3])
+        self.crystal.addAtom('Pt',[0.,0.,0.],0.1,0.1,1.)
+        self.crystal.setEnergy(E*1e3)
+        
+        self.ubCal = HKLVlieg.UBCalculator(self.crystal,E)
+        self.ubCal.defaultU()
+        self.angles = HKLVlieg.VliegAngles(self.ubCal)
+        
+        if 'crystal' in lattice:
+            idx = self.crystalparams.crystalComboBox.findText(lattice['crystal'],qt.Qt.MatchFixedString)
+            if idx == -1:
+                qt.QMessageBox.warning(self,"Did not find crystal","Can not find crystal <%s> \nException occured during read of configfile %s,\nException:\n%s" % (unitcellsconfigfile,traceback.format_exc()))
+            else:
+                self.crystalparams.crystalComboBox.setCurrentIndex(idx)
+                self.crystalparams.onSwitchCrystal(idx)
+                #self.crystal = self.crystalparams.getCrystal()
+
+        if latticeoverride:
+            print('foo')
+            self.crystal.setLattice([a1,a2,a3],[alpha1,alpha2,alpha3])
+        
+
+        if 'poni' in machine:
+            if machine['poni']:
+                self.detectorCal.load(machine['poni'])
+                self.ubCal.setLambda(self.detectorCal.get_wavelength()*1e10)
+                
+            else:
+                self.detectorCal.setFit2D(sdd*1e3,cpx,cpy,pixelX=pixelsize*1e6, pixelY=pixelsize*1e6)
+                self.detectorCal.set_wavelength(self.ubCal.getLambda()*1e-10)
+                self.detectorCal.detector.shape = (2880,2880) # Perkin 
+                
+        else:
+            self.detectorCal.setFit2D(sdd*1e3,cpx,cpy,pixelX=pixelsize*1e6, pixelY=pixelsize*1e6)
+            self.detectorCal.set_wavelength(self.ubCal.getLambda()*1e-10)
+            self.detectorCal.detector.shape = (2880,2880)
+            
+        self.detectorCal.setAzimuthalReference(self.azimuth)
+        self.detectorCal.setPolarization(self.polaxis,self.polfactor)
+        
+        fit2dCal = self.detectorCal.getFit2D()
+
+        paramlist = [self.ubCal.getEnergy(),self.mu,fit2dCal['directDist']/1e3,
+                     fit2dCal['pixelX']*1e-6,[fit2dCal['centerX'],fit2dCal['centerY']],self.polaxis
+                     ,self.polfactor,self.azimuth,self.chi,self.phi]
+        self.crystalparams.setValues(self.crystal,self.n)
+        self.machineParams.setValues(paramlist)
+        
+        
+    
+    
+
+
+class DataBase(qt.QMainWindow):
+    
+    def __init__(self, plot, parent=None):
+        qt.QMainWindow.__init__(self, parent)
+        self.nxfile = None
+        self.filedialogdir = os.getcwd()
+        self.plot = plot
+        
+        self.view = silx.gui.hdf5.Hdf5TreeView()
+        self.view.setSortingEnabled(True)
+        
+        #self.view.addContextMenuCallback(self.nexus_treeview_callback)
+        #self.hdf5model = self.view.findHdf5TreeModel()
+        
+        customModel = Hdf5TreeModel
+        customModel.NAME_COLUMN = 0
+        customModel.DESCRIPTION_COLUMN = 1
+        customModel.VALUE_COLUMN = 2
+        customModel.SHAPE_COLUMN = 3
+        customModel.TYPE_COLUMN = 4
+        customModel.NODE_COLUMN = 5
+        customModel.LINK_COLUMN = 6
+        
+        self.hdf5model = customModel(self.view)
+        self.view.setModel(self.hdf5model)
+
+        self.dataviewer = DataViewerFrame.DataViewerFrame()
+        self.dataviewerDialog = qt.QDialog(self)
+        dvlayout = qt.QVBoxLayout()
+        dvlayout.addWidget(self.dataviewer)
+        self.dataviewerDialog.setLayout(dvlayout)
+        self.dataviewerDialog.setModal(False)
+        
+        self.view.setExpandsOnDoubleClick(False)
+        self.hdf5model.setFileMoveEnabled(True)
+        #self.__treeModelSorted = silx.gui.hdf5.NexusSortFilterProxyModel(self.view)
+        #self.__treeModelSorted.setSourceModel(self.hdf5model)
+        #self.__treeModelSorted.sort(0, qt.Qt.AscendingOrder)
+        #self.__treeModelSorted.setSortCaseSensitivity(qt.Qt.CaseInsensitive)
+
+        #self.hdfTreeView.setModel(self.__treeModelSorted)
+        
+        self.view.doubleClicked.connect(self._onNEXUSDoubleClicked)
+        self.view.addContextMenuCallback(self.nexus_treeview_callback)
+        
+        self.temp_directory = tempfile.TemporaryDirectory(dir=os.path.join(os.getcwd()))
+        tempfilepath = os.path.join(self.temp_directory.name,"orgui_database.h5")
+        self.createNewDBFile(tempfilepath)
+        #self.add_nxdict(gauss)
+        #self.add_nxdict(gauss)
+        self.setCentralWidget(self.view)
+        
+        toolbar = qt.QToolBar("Database toolbar",self)
+        
+        loadDatabaseAct = toolbar.addAction(icons.getQIcon("document-open"),"Open orgui database")
+        loadDatabaseAct.triggered.connect(self.onOpenDatabase)
+        
+        savenewact = toolbar.addAction(icons.getQIcon("layer-nx"),"Select orgui database location")
+        savenewact.triggered.connect(self.onSaveNewDBFile)
+                
+        saveact = toolbar.addAction(icons.getQIcon("document-save"),"Save orgui database")
+        saveact.triggered.connect(self.onSaveDBFile)
+        
+        self.addToolBar(toolbar)
+        
+    def _onNEXUSDoubleClicked(self,index): # ToDo add try except with popup message!
+        nodes = list(self.view.selectedH5Nodes())
+        if len(nodes) > 0:
+            obj = nodes[0]
+            if obj.ntype is h5py.Dataset:
+                roi_node = self.get_roinode(obj.h5py_object)
+                if roi_node is not None:
+                    self.plot_signal_callback(roi_node, obj)
+                    return
+            self.plot_default(obj.h5py_object)
+                
+    def plot_default(self, h5py_object):
+        try:
+            nxdat = nxdata.get_default(h5py_object)
+            #print(nxdat.axes, nxdat.signal, nxdat.title)
+            #print(nxdat.signal_name, nxdat.errors, nxdat.axes_names)
+            if nxdat is not None and len(nxdat.axes) == 1:
+                self.plot.addCurve(nxdat.axes[0], nxdat.signal, legend=nxdat.title, xlabel=nxdat.axes_names[0], ylabel=nxdat.signal_name, yerror=nxdat.errors)
+        except Exception as e:
+            traceback.print_exc()
+            print("Cannot plot data: %s" % e)
+
+    def get_roinode(self, obj):
+        if silx.io.utils.get_h5_class(obj) is None:
+            return None
+            
+        while(obj.name != '/'):
+            meta = obj.attrs.get('orgui_meta', False)
+            if meta and meta == 'roi':
+                return obj
+            obj = obj.parent
+            
+    def get_scannode(self, obj):
+        if silx.io.utils.get_h5_class(obj) is None:
+            return None
+            
+        while(obj.name != '/'):
+            meta = obj.attrs.get('orgui_meta', False)
+            if meta and meta == 'scan':
+                return obj
+            obj = obj.parent
+            
+    def nexus_treeview_callback(self,event):
+        objects = list(event.source().selectedH5Nodes())
+        obj = objects[0]  # for single selection
+        menu = event.menu()
+        action = qt.QAction("Refresh", menu)
+        action.triggered.connect(lambda:  self.hdf5model.synchronizeH5pyObject(obj))
+        menu.addAction(action)
+        action = qt.QAction("details", menu)
+        action.triggered.connect(lambda:  self.view_data_callback(obj))
+        menu.addAction(action)
+        
+        if obj.ntype is h5py.Dataset:
+            roi_node = self.get_roinode(obj.h5py_object)
+            if roi_node is not None:
+                action = qt.QAction("plot %s" % obj.name, menu)
+                action.triggered.connect(lambda:  self.plot_signal_callback(roi_node, obj))
+                menu.addAction(action)
+        
+        if obj.ntype is h5py.Group:
+            meta = obj.h5py_object.attrs.get('orgui_meta', False)
+            if meta and meta == 'roi':
+                action = qt.QAction("rename", menu)
+                action.triggered.connect(lambda:  self.onRenameNode(obj.h5py_object))
+                menu.addAction(action)
+                menu.addSeparator()
+                action = qt.QAction("delete", menu)
+                action.triggered.connect(lambda:  self.delete_node(obj.h5py_object))
+                menu.addAction(action)
+                
+            if meta and meta == 'scan':
+                menu.addSeparator()
+                action = qt.QAction("delete", menu)
+                action.triggered.connect(lambda:  self.onDeleteScan(obj.h5py_object))
+                menu.addAction(action)
+            
+        """    
+        if obj.ntype is h5py.File:
+            action = qt.QAction("remove", menu)
+            action.triggered.connect(lambda:  self._onCloseFile())
+            menu.addAction(action)
+        """
+    def plot_signal_callback(self, roi_node, dataset):
+        try:
+            nxdat = nxdata.get_default(roi_node)
+            data = dataset.h5py_object[()]
+            #print(nxdat.axes, nxdat.signal, nxdat.title)
+            #print(nxdat.signal_name, nxdat.errors, nxdat.axes_names)
+            if nxdat is not None and len(nxdat.axes) == 1:
+                self.plot.addCurve(nxdat.axes[0], data, legend=nxdat.title + "_" + dataset.name, xlabel=nxdat.axes_names[0], ylabel=dataset.name)
+        except Exception as e:
+            traceback.print_exc()
+            print("Cannot plot data: %s" % e)
+    
+        
+        
+    def view_data_callback(self,obj):
+        self.dataviewer.setData(obj)
+        self.dataviewerDialog.open()
+        
+    def onSaveNewDBFile(self):
+        fileTypeDict = {'NEXUS Files (*.h5)': '.h5', 'All files (*)': '' }
+        fileTypeFilter = ""
+        for f in fileTypeDict:
+            fileTypeFilter += f + ";;"
+            
+        filename, filetype = qt.QFileDialog.getSaveFileName(self,"Select database location",
+                                                  self.filedialogdir,
+                                                  fileTypeFilter[:-2])
+        if filename == '':
+            return
+        
+        self.filedialogdir = os.path.splitext(filename)[0]
+        #filename += fileTypeDict[filetype]
+        self.saveNewDBFile(filename)
+        
+    def onSaveDBFile(self):
+        fileTypeDict = {'NEXUS Files (*.h5)': '.h5', 'All files (*)': '' }
+        fileTypeFilter = ""
+        for f in fileTypeDict:
+            fileTypeFilter += f + ";;"
+            
+        filename, filetype = qt.QFileDialog.getSaveFileName(self,"Save database",
+                                                  self.filedialogdir,
+                                                  fileTypeFilter[:-2])
+        if filename == '':
+            return
+        
+        self.filedialogdir = os.path.splitext(filename)[0]
+        #filename += fileTypeDict[filetype]
+        self.saveDBFile(filename)
+        
+    def onOpenDatabase(self):
+        fileTypeDict = {'NEXUS Files (*.h5)': '.h5', 'All files (*)': '' }
+        fileTypeFilter = ""
+        for f in fileTypeDict:
+            fileTypeFilter += f + ";;"
+            
+        filename, filetype = qt.QFileDialog.getOpenFileName(self,"Save database",
+                                                  self.filedialogdir,
+                                                  fileTypeFilter[:-2])
+        if filename == '':
+            return
+        
+        self.filedialogdir = os.path.splitext(filename)[0]
+        #filename += fileTypeDict[filetype]
+        try:
+            self.openDBFile(filename)
+        except:
+            msgbox = qt.QMessageBox(qt.QMessageBox.Critical,'Cannot open db file', 
+            'Cannot open db file %s.' % filename,
+            qt.QMessageBox.Ok, self)
+            msgbox.setDetailedText(traceback.format_exc())
+            clickedbutton = msgbox.exec()
+        
+        
+    def saveNewDBFile(self, filename):
+        alldata = nxtodict(self.nxfile)
+        self.createNewDBFile(filename, alldata)
+        
+    def saveDBFile(self, filename):
+        alldata = nxtodict(self.nxfile)
+        dicttonx(alldata, filename)
+        
+    def createNewDBFile(self, filename, datadict=None):
+        if self.nxfile is not None:
+            while(self.hdf5model.hasPendingOperations()):
+                qt.QApplication.processEvents()
+                time.sleep(0.01)
+            self.hdf5model.removeH5pyObject(self.nxfile)
+            self.nxfile.close()
+            self.nxfile = None
+            if hasattr(self, "temp_directory"):
+                del self.temp_directory
+
+        fileattrs = {"@NX_class": u"NXroot",
+                     "@creator": u"orGUI version %s" % __version__,
+                     "@file_name": str(os.path.basename(filename)),
+                     "@file_time": datetime.datetime.utcnow().isoformat()}
+        if datadict is None:
+            datadict = fileattrs
+        else:
+            datadict.update(fileattrs)
+        try:
+            dicttonx(datadict, filename)
+            self.openDBFile(filename)
+        except:
+            msgbox = qt.QMessageBox(qt.QMessageBox.Critical,'Cannot create db file', 
+            'Cannot create file %s.' % filename,
+            qt.QMessageBox.Ok, self)
+            msgbox.setDetailedText(traceback.format_exc())
+            clickedbutton = msgbox.exec()
+        
+    def openDBFile(self, filename):
+        if self.nxfile is not None:
+            self.hdf5model.removeH5pyObject(self.nxfile)
+            self.nxfile.close()
+            if hasattr(self, "temp_directory"):
+                del self.temp_directory
+        self.nxfile = silx.io.h5py_utils.File(filename,'a')
+        self._filepath = filename
+        while(self.hdf5model.hasPendingOperations()):
+            qt.QApplication.processEvents()
+            time.sleep(0.01)
+        self.hdf5model.insertH5pyObject(self.nxfile)
+        self.view.expandToDepth(0)
+
+    def add_nxdict(self, nxentry):
+        if self.nxfile is None:
+            raise Exception("No database file open.")
+        dicttonx(nxentry, self.nxfile, update_mode='add')
+        while(self.hdf5model.hasPendingOperations()):
+            qt.QApplication.processEvents()
+            time.sleep(0.01)
+        self.hdf5model.synchronizeH5pyObject(self.nxfile)
+        self.view.expandToDepth(0)
+        
+    def onDeleteScan(self, obj):
+        btn = qt.QMessageBox.question(self,"Delete scan?","Are you sure that you want to delete %s from the orgui database?" % obj.name.split("/")[-1])
+        if btn == qt.QMessageBox.Yes:
+            self.delete_node(obj)
+        
+    def delete_node(self, obj):
+        basename = obj.name.split("/")[-1]
+        objpar = obj.parent
+        del objpar[basename]
+        while(self.hdf5model.hasPendingOperations()):
+            qt.QApplication.processEvents()
+            time.sleep(0.01)
+        self.hdf5model.synchronizeH5pyObject(self.nxfile)
+        self.view.expandToDepth(0)
+        
+    def onRenameNode(self, obj):
+        basename = obj.name.split("/")[-1]
+        newname, success = qt.QInputDialog.getText(self,"Rename NEXUS node",
+                               "New name:", qt.QLineEdit.EchoMode.Normal,
+                               basename)
+        if success and newname != '':
+            self.rename_node(obj, newname)
+                               
+    def rename_node(self, obj, newname):
+        basename = obj.name.split("/")[-1]
+        objpar = obj.parent
+        objpar.move(basename, newname)
+        while(self.hdf5model.hasPendingOperations()):
+            qt.QApplication.processEvents()
+            time.sleep(0.01)
+        self.hdf5model.synchronizeH5pyObject(self.nxfile)
+        self.view.expandToDepth(0)
+        
+        
+    def close(self):
+        if self.nxfile is not None:
+            self.hdf5model.removeH5pyObject(self.nxfile)
+            self.nxfile.close()
+            self.nxfile = None
+            if hasattr(self, "temp_directory"):
+                del self.temp_directory
+        
+    
+    
+