initial fitting updates. Merged new (pre-single-crystal) code from

master

.gitignore

@@ -17,7 +17,10 @@ __pycache__
 .venv*
 .coverage
 .pyc
-#resources.py
+resources.py
+
+# Pytest
+.tests
 
 # C++
 
@@ -40,6 +43,8 @@ build
 *.user
 settings.ini*
 .ci/
+ci/
+ci_*/
 .idea/
 .build/
 temp/

CHANGELOG.md

@@ -4,39 +4,39 @@ This is a test version of EasyDiffraction with improved GUI and overall performa
 
 ### Bug Fixes
 
-- The correct x-axis title is now displayed for graphs with TOF data
-- The startup splash screen now appears before the calculation libraries are loaded
+- The correct x-axis title is now displayed for graphs with TOF data.
+- The startup splash screen now appears before the calculation libraries are loaded.
 
 # Version 0.9.4 (26 Jun 2024)
 
 This is a test version of EasyDiffraction with improved GUI and overall performance. This version temporarily does not use the EasyScience framework, contains only CrysPy as calculation engine and uses only Lmfit for minimization.  
 
 ### New Features
 
-- Point background is now implemented for time-of-flight (TOF) type of experiments
+- Point background is now implemented for time-of-flight (TOF) type of experiments.
 
 # Version 0.9.3 (21 Jun 2024)
 
 This is a test version of EasyDiffraction with improved GUI and overall performance. This version temporarily does not use the EasyScience framework, contains only CrysPy as calculation engine and uses only Lmfit for minimization.  
 
 ### Bug Fixes
 
-- The package for Snap Store (Linux) has been added back
+- The package for Snap Store (Linux) has been added back.
 
 # Version 0.9.2 (20 Jun 2024)
 
 This is a test version of EasyDiffraction with improved GUI and overall performance. This version temporarily does not use the EasyScience framework, contains only CrysPy as calculation engine and uses only Lmfit for minimization.  
 
 ### New Features
 
-- The analysis page now has an _html_-based analysis summary
-- The CIF-based report on the Summary page has now been moved from _Main View_ to _Sidebar_ (`Text mode` tab)
-- User can now save the analysis summary in _html_ format
-- Installers for macOS and Windows are now signed
+- The analysis page now has an _html_-based analysis summary.
+- The CIF-based report on the Summary page has now been moved from _Main View_ to _Sidebar_ (`Text mode` tab).
+- User can now save the analysis summary in _html_ format.
+- Installers for macOS and Windows are now signed.
 
 ### Bug Fixes
 
-- Measured and processed TOF data are now correctly displayed on the Summary page
+- Measured and processed TOF data are now correctly displayed on the Summary page.
 
 # Version 0.9.1-alpha0 (29 May 2024)
 

easyDiffractionApp/Logic/Experiment.py

@@ -161,6 +161,7 @@ def __init__(self, parent, interface=None):
 
         self._chartRanges = []
 
+    @Property('QVariant', constant=True)
     def job(self):
         return self._job
 
@@ -255,6 +256,8 @@ def loadExperimentsFromFiles(self, fpaths):
 
     def loadExperimentFromCifString(self, cifString="", job_name=""):
         console.debug(f"Loading experiment(s) from: {job_name}")
+        # assure we reference the right interface
+        self._interface = self._job.interface
         self.loadExperimentsFromEdCif(cifString)
 
         self._job.add_experiment_from_string(cifString)
@@ -268,8 +271,9 @@ def loadExperimentFromCifString(self, cifString="", job_name=""):
         self._currentIndex = len(self._dataBlocksNoMeas) - 1
         if not self.defined:
             self.defined = bool(len(self._dataBlocksNoMeas))
+
         self.dataBlocksChanged.emit()
-        self._job.interface = self._interface
+        #self._job.interface = self._interface
 
     def jobToBlock(self, job=None, name=None):
         '''
@@ -1339,28 +1343,27 @@ def isSpinPolarized(self):
     def runProfileCalculations(self):
 
         # shove it all into the calculator.
+        # result = self._interface.calculate_profile()
+
+        # console.debug(formatMsg('sub', 'Profle calculations', 'finished'))
 
-        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)
+        # 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)
 
-        console.debug(formatMsg('sub', 'Profle calculations', 'finished'))
+        # gofLastIter = self._proxy.fitting.chiSq  # NEED FIX
 
-        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)
+        _ = self._job.calculate_profile() # this fills out calculator _inOutDict
 
-        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:
         #     gofStart = self._proxy.fitting.chiSqStart # NEED FIX
         #     self._proxy.status.goodnessOfFit = f'{gofStart:0.2f} → {gofLastIter:0.2f}'  # NEED move to connection
         # if not self._proxy.fitting._freezeChiSqStart:
         #     self._proxy.fitting.chiSqStart = self._proxy.fitting.chiSq
+        pass
 
     def setMeasuredArraysForSingleExperiment(self, idx):
         diffrn_radiation_type = self.dataBlocksNoMeas[idx]['params']['_diffrn_radiation']['type']['value']

easyDiffractionApp/Logic/Fitting2.py

@@ -46,7 +46,7 @@ def __init__(self, proxy=None, interface=None):
         self.interface = interface
         # self.fitter = CoreFitter(self.parent.sample(), self.interface.fit_func)
         # self.fitter = CoreFitter(self.parent.experiment.job(), self.parent.experiment.job().create_simulation)
-        self.fitter = CoreFitter(self.parent.experiment.job(), self.interface.fit_func)
+        self.fitter = CoreFitter(self.parent.experiment.job, self.interface.fit_func)
 
         # Multithreading
         # self._fitter_thread = None
@@ -227,7 +227,7 @@ def onFailed(self, ex):
     @Slot()
     def startStop(self):
         # self.data = self.parent.pdata()
-        name = 'pd_' + self.parent.experiment.job().experiment.name
+        name = 'pd_' + self.parent.experiment.job.experiment.name
         self.data = self.interface.data()._inOutDict[name]
         if self.use_threading:
             if not self.fit_thread.is_alive():

easyDiffractionApp/Logic/Model.py

@@ -183,7 +183,7 @@ def addDefaultPhase(self):
     def atomData(self, typeSymbol, key):
         if typeSymbol == '':
             return ''
-        typeSymbol = re.sub(r'[0-9]', '', typeSymbol)  # '162Dy' -> 'Dy'
+        typeSymbol = re.sub(r'[0-9\+\-]', '', typeSymbol)  # '162Dy' -> 'Dy', 'Co2+' -> 'Co'
         if key == 'color':
             return COLOR_TABLE[typeSymbol]
         try:
@@ -620,7 +620,6 @@ def removeDataBlockLoopRow(self, category, rowIndex):
         console.debug(formatMsg('sub', 'Intern dict', 'removed', f'{block}[{blockIdx}].{category}[{rowIndex}]'))
 
     def appendDataBlockLoopRow(self, category):
-        print("\nappendDataBlockLoopRow\n")
         block = 'model'
         blockIdx = self._currentIndex
 

easyDiffractionApp/Logic/Project.py

@@ -1,6 +1,6 @@
 # SPDX-FileCopyrightText: 2023 EasyDiffraction contributors
 # SPDX-License-Identifier: BSD-3-Clause
-# © © 2023 Contributors to the EasyDiffraction project <https://github.com/easyscience/EasyDiffractionApp>
+# © 2023 Contributors to the EasyDiffraction project <https://github.com/easyscience/EasyDiffractionApp>
 
 import os
 import time
@@ -13,7 +13,7 @@
 from easydiffraction.io.cif import dataBlockToCif
 from easydiffraction.io.cif import cifV2ToV1
 from EasyApp.Logic.Logging import console
-
+from Logic.Helpers import formatMsg
 
 
 _EMPTY_DATA = {
@@ -76,11 +76,11 @@
         'description': 'neutrons, powder, time-of-flight, SEPD@Argonne',
         'path': ':/Examples/Si_SEPD@Argonne/project.cif'
      },
-     {
-        'name': 'CeCuAl3 (Polaris)',
-        'description': 'neutrons, powder, time-of-flight, Polaris@ISIS',
-        'path': ':/Examples/CeCuAl3_Polaris@ISIS/project.cif'
-     },
+     #{
+     #   'name': 'CeCuAl3 (Polaris)',
+     #   'description': 'neutrons, powder, time-of-flight, Polaris@ISIS',
+     #   'path': ':/Examples/CeCuAl3_Polaris@ISIS/project.cif'
+     #},
      {
         'name': 'Na2Ca3Al2F14 (Osiris)',
         'description': 'neutrons, powder, time-of-flight, Osiris@ISIS',
@@ -91,6 +91,16 @@
         'description': 'neutrons, powder, time-of-flight, WISH@ISIS',
         'path': ':/Examples/Na2Ca3Al2F14_WISH@ISIS/project.cif'
      },
+     {
+        'name': 'CeO2 (iMATERIA)',
+        'description': 'neutrons, powder, time-of-flight, iMATERIA@J-PARC',
+        'path': ':/Examples/CeO2_iMATERIA@J-PARC/project.cif'
+     },
+     {
+        'name': 'Tb2Ti2O7 (HEiDi)',
+        'description': 'neutrons, single crystal, constant wavelength, HEiDi@MLZ',
+        'path': ':/Examples/Tb2Ti2O7_HEiDi@MLZ/project.cif'
+     },
      #{
      #    'name': 'Co2SiO4-Mult-Phases',
      #    'description': 'neutrons, powder, constant wavelength, D20@ILL, 2 phases',
@@ -121,6 +131,7 @@ class Project(QObject):
     def __init__(self, parent=None):
         super().__init__(parent)
         self._proxy = parent
+        self._recent = []
         self.resetAll()
 
     @Slot()
@@ -130,7 +141,6 @@ def resetAll(self):
         self._examples = _EXAMPLES
         self._created = False
         self._needSave = False
-        self._recent = []
         self._isExample = False
 
         self._location = str(Path.home())

pyproject.toml

@@ -35,6 +35,7 @@ dependencies = [
     'toml',
     'darkdetect',
     'numdifftools',
+    'funcy',
     'cryspy @ git+https://github.com/ikibalin/cryspy.git@beta',
     'EasyApp @ git+https://github.com/easyscience/EasyApp.git@beta',
     'easyDiffraction @ git+https://github.com/easyscience/EasyDiffractionLib.git@new_param'

tools/Scripts/Config.py

@@ -70,13 +70,13 @@ def __getitem__(self, key):
         return self.__dict__[key]
 
     def matrixOs(self, matrix_os):
-        if matrix_os is None:
-            return None
-        if 'ubuntu-24.04' in matrix_os:
-            matrix_os = 'ubuntu-22.04'  # NEED FIX: Temporary solution to test the 22.04 build on 24.04
-        elif 'flyci' in matrix_os:
-            matrix_os = matrix_os.removeprefix('flyci-')  # Simplify the default flyci name
-            matrix_os = matrix_os.removesuffix('-m2')  # Simplify the default flyci name
+        #if matrix_os is None:
+        #    return None
+        #if 'ubuntu-24.04' in matrix_os:
+        #    matrix_os = 'ubuntu-22.04'  # NEED FIX: Temporary solution to test the 22.04 build on 24.04
+        #elif 'flyci' in matrix_os:
+        #    matrix_os = matrix_os.removeprefix('flyci-')  # Simplify the default flyci name
+        #    matrix_os = matrix_os.removesuffix('-m2')  # Simplify the default flyci name
         return matrix_os
 
     # https://doc.qt.io/qtinstallerframework/scripting.html

tools/Scripts/FreezeApp.py

@@ -131,6 +131,7 @@ def runPyInstaller():
             '--clean',                              # Clean PyInstaller cache and remove temporary files before building
             '--windowed',                           # Windows and Mac OS X: do not provide a console window for standard i/o.
             '--onedir',                             # Create a one-folder bundle containing an executable (default)
+            #'--target-architecture', 'universal2', # Target architecture (macOS only; valid values: x86_64, arm64, universal2). Error: _multiarray_tests.cpython-311-darwin.so is not a fat binary! (i.e. not multi-architecture)
             #'--specpath', workDirPath(),           # Folder to store the generated spec file (default: current directory)
             '--distpath', CONFIG.dist_dir,          # Where to put the bundled app (default: ./dist)
             '--workpath', CONFIG.build_dir,         # Where to put all the temporary work files, .log, .pyz and etc. (default: ./build)

tools/Scripts/Functions.py

@@ -91,7 +91,6 @@ def installSilently(installer, silent_script, sudo=False):
         args = [installer, '--verbose', '--script', silent_script]
         if sudo:
             args = ['sudo', *args]
-
         run(*args)
     except Exception as exception:
         printFailMessage(message, exception)