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All the necessary files. Small updates to GUI.py and temCalcs.py

Author: din14970

Diff for: GUI.py

@@ -20,7 +20,7 @@ class App(QMainWindow):
 
     def __init__(self):
         super().__init__()
-        self.title = "TEMTilt v0.01 BETA"
+        self.title = "ALPHABETA v0.01 BETA"
         #self.left = 50
         #self.top = 50
         #self.width = 640
@@ -278,6 +278,15 @@ def __init__(self, caller):
         self.kvbox.setSizePolicy(sp)
         temlayout.addWidget(self.kvbox, 1, 6)
 
+        #the ewald sphere radius. The angle must be added later when you update the field
+        self.eslbl = QLabel(u"K0")
+        self.eslbl.setToolTip("The radius of the Ewald sphere\n1/electron wavelength")
+        temlayout.addWidget(self.eslbl, 1, 7)
+        self.k0view = QLineEdit(self)
+        self.k0view.setReadOnly(True)
+        self.k0view.setSizePolicy(sp)
+        temlayout.addWidget(self.k0view, 1, 8)
+        
         ######The stage menu#################
         #add the stage dropdown list
         yoffset = 50
@@ -493,6 +502,7 @@ def deleteDetector(self):
     def updateVoltage(self, value):
         try:
             self.currentTEM().setKv(value)
+            self.updateK0()
         except:
             pass
 
@@ -554,6 +564,13 @@ def updateTheta(self):
         except: #if no mag data can be found
             self.thetaview.setText("")
 
+    def updateK0(self):
+        try:
+            self.k0view.setText(u"%s 1/\u212B" %(round(self.currentTEM().getEwaldR(units = "angstrom"), 2)))
+        except:
+            #when the current TEM is none
+            self.k0view.setText("")
+    
     def currentTEM(self):
         if tc.microscopes:
             return tc.getMicroscope(self.temlist.currentText())
@@ -698,6 +715,7 @@ def updatebuttons(self):
             self.edittembut.hide()
             self.deltembut.hide()
             self.kvbox.hide()
+            self.k0view.hide()
             #stage buttons
             self.stagelist.hide()
             self.adstagbut.hide()
@@ -721,8 +739,10 @@ def updatebuttons(self):
             self.edittembut.show()
             self.deltembut.show()
             self.kvbox.show()
+            self.k0view.show()
             #update the kV box
             self.kvbox.setValue(self.currentTEM().getKv())
+            self.updateK0()
 
             #stage buttons
             self.stagelist.show()
@@ -807,7 +827,7 @@ def __init__(self, caller):
         self.adstrucbut = self.button(logo=".\Images\plus.png", hint = "Add new structure",  action = self.createStructure)
         self.editstrucbut = self.button(logo = ".\Images\edit.png", hint = "Edit structure",  action = self.editStructure)
         self.delstrucbut = self.button(logo=".\Images\delete-icon.png", hint = "Delete structure",  action = self.deleteStructure)
-        self.calcbut = self.button(logo=".\Images\calc.png", hint = "Crystallography calculator",  action = self.showCalculator)
+        self.calcbut = self.button(logo=".\Images\wizard.png", hint = "Indexing wizard",  action = self.showWizard)
 
         layout.addWidget(self.adstrucbut, 1, 2)
         layout.addWidget(self.editstrucbut, 1, 3)
@@ -903,8 +923,8 @@ def deleteStructure(self):
             tc.removeStructure(nt)
             self.updateAll()
 
-    def showCalculator(self):
-        pass
+    def showWizard(self):
+        indexingDialog.getInfo(caller = self.caller)
 
     def currentStruc(self):
         try:
@@ -2288,7 +2308,8 @@ def getActiveRow(self):
             return None
 
     def showHelp(self):
-        self.testIndexation()
+        QMessageBox.information(self, " ", "Tilt to some zone axis and capture the diffraction pattern. Of 2 non-colinear reflections (hkl) measure:\n-the distance between (000) and (hkl) in 1/nm.\n-the angle between the detector X-axis and the line that connects (000) and (hkl).\nNote that the X-axis points to the right and that positive angles are clockwise.")
+        #self.testIndexation()
 
     def testIndexation(self):
         self.l1box.setValue(5.6)
@@ -2401,7 +2422,37 @@ def getres(self):
             else:
                 values.append(None)
         return values
-    
+
+class indexingDialog(Dialog):
+    """Opens a window with only an indexing wizard widget"""
+    def __init__(self, caller, windowtitle = "Indexing wizard",  **kwargs):
+        super(indexingDialog, self).__init__()
+        #caller is the mainwindow app for access to current settings if necessary
+        self.caller = caller
+        struc = caller.getCurrentStructure()
+        
+        #the wizard
+        self.wiz = indexWizard(struc)
+        
+        #the button box
+        self.buttonBox = QDialogButtonBox(QDialogButtonBox.Cancel)
+        self.buttonBox.rejected.connect(self.reject)
+        
+        self.makeLayout()
+        self.setWindowTitle(windowtitle)
+        
+    def makeLayout(self):
+        mainLayout = QVBoxLayout()
+        mainLayout.addWidget(self.wiz)
+        mainLayout.addWidget(self.buttonBox)
+        mainLayout.setSizeConstraint(mainLayout.SetFixedSize)
+        self.setLayout(mainLayout) 
+        
+    # static method doesn't have to do much in this case
+    @staticmethod
+    def getInfo(**kwargs):
+        dialog = indexingDialog(**kwargs)
+        result = dialog.exec_()
 
 class microscopeDialog(Dialog):
 
@@ -2609,7 +2660,7 @@ def createFormGroupBox(self, name = "", alpha = 0.0, alphamin = -30.0, alphamax=
         qbutton = QPushButton("", self)
         qbutton.setToolTip("What is this?")
         qbutton.setIcon(QIcon(".\Images\question.png"))
-        #qbutton.clicked.connect(action)
+        qbutton.clicked.connect(self.showHelp)
         qbutton.resize(24+6, 24+6)
         qbutton.setIconSize(QSize(24,24))
         qbutton.setSizePolicy(sp)
@@ -2701,6 +2752,9 @@ def createFormGroupBox(self, name = "", alpha = 0.0, alphamin = -30.0, alphamax=
 
         self.formGroupBox.setLayout(layout)
 
+    def showHelp(self):
+        QMessageBox.information(self, " ", "The \u03b1-axis (X) runs along the double-tilt holder main axis pointed out of the microscope, the absolute Z axis is pointed down the column. The \u03b2-axis (Y) is defined by X x Y = Z at (0,0) tilt. Rotations follow the right hand rule.\n\nIf your holder doesn't follow these conventions, use the 'Reversed?' checkboxes appropriately.")
+    
     def anglemaxupdate(self):
         self.alphabox.setMaximum(self.alphamaxbox.value())
         self.alphabox.setMinimum(self.alphaminbox.value())

Diff for: GUI.spec

@@ -0,0 +1,38 @@
+# -*- mode: python -*-
+import sys
+import os
+sys.setrecursionlimit(5000)
+
+block_cipher = None
+
+options = [ ('v', None, 'OPTION') ]
+
+a = Analysis(['GUI.py'],
+             pathex=['C:\\users\\ncautaer\\desktop\\Python Experience\\TEM calcs v2'],
+             binaries=[],
+             datas = [],
+             #datas=[('\Images\*.png', 'Images')],
+             hiddenimports=['scipy._lib.messagestream'],
+             hookspath=[],
+             runtime_hooks=[],
+             excludes=[],
+             win_no_prefer_redirects=False,
+             win_private_assemblies=False,
+             cipher=block_cipher)
+pyz = PYZ(a.pure, a.zipped_data,
+             cipher=block_cipher)
+exe = EXE(pyz,
+          a.scripts,
+          exclude_binaries=True,
+          name='GUI',
+          debug=False,
+          strip=False,
+          upx=True,
+          console=True )
+coll = COLLECT(exe,
+               a.binaries,
+               a.zipfiles,
+               a.datas,
+               strip=False,
+               upx=True,
+               name='GUI')

Diff for: Images/Icons.pptx

@@ -0,0 +1,13 @@
+The working combination for compilation:
+- I installed pipenv (as admin) and created a virtual environment for my folder
+- In the virtual environment, I installed scipy, numpy, matplotlib, pyqt5, and pyinstaller using:
+pyenv run pip package_name
+- I ran: pipenv run pyinstaller GUI.py
+- This created a spec file. I modified the spec file to include verbose and to include scipy.messagebox as hiddenimport (whatever that does, it was needed)
+- I ran the command (as admin) in windows powershell:
+pipenv run pyinstaller --onedir --noupx --clean GUI.py
+- This gave me a permission error
+- I ran it again and there was no problem anymore 
+- I mannually coppied the Images folder into the generated dist folder. This finally got me a working exe.
+
+Niels Cautaerts, 18/05/18

Diff for: Images/Nespolo_zone_axis.pdf

@@ -2,9 +2,7 @@
 
 import numpy as np
 import math as ma
-import pandas as pd
 import matplotlib.pyplot as plt
-import pickle
 import re
 from fractions import Fraction
 import math