Merge pull request #1815 from kif/1808_calib2

Alternative visulalization of geometry

pyFAI/app/calib2.py

@@ -28,7 +28,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "21/01/2020"
+__date__ = "24/02/2023"
 __status__ = "production"
 
 import os
@@ -569,7 +569,7 @@ def main():
         silx.config.DEFAULT_PLOT_BACKEND = "opengl"
 
     # Make sure matplotlib is loaded first by silx
-    import silx.gui.plot.matplotlib
+    import silx.gui.utils.matplotlib
     from pyFAI.gui.CalibrationWindow import CalibrationWindow
     from pyFAI.gui.CalibrationContext import CalibrationContext
 

pyFAI/azimuthalIntegrator.py

@@ -30,7 +30,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "22/02/2023"
+__date__ = "24/02/2023"
 __status__ = "stable"
 __docformat__ = 'restructuredtext'
 
@@ -2218,7 +2218,7 @@ def integrate2d_ng(self, data, npt_rad, npt_azim=360,
         norm2d = None
         var2d = None
 
-        if method.algo_lower in ("csr", "lut"):
+        if method.algo_lower in ("csr", "csc", "lut"):
             intpl = None
             cython_method = IntegrationMethod.select_method(method.dimension, method.split_lower, method.algo_lower, "cython")[0]
             if cython_method not in self.engines:
@@ -2936,14 +2936,14 @@ def sigma_clip_legacy(self, data, npt_rad=1024, npt_azim=512,
         :param metadata: any other metadata,
         :type metadata: JSON serializable dict
         :param safe: unset to save some checks on sparse matrix shape/content.
-        :return: Integrate1D-like result
+        :kwargs: unused, just for signature compatibility when used within Worker.
+        :return: Integrate1D like result like
 
         Nota: The initial 2D-integration requires pixel splitting
         """
-        #compatibility layer with sigma_clip_ng
+        # compatibility layer with sigma_clip_ng
         if "npt" in kwargs:
             npt_rad = kwargs["npt"]
-
         # We use NaN as dummies
         if dummy is None:
             dummy = numpy.NaN
@@ -2971,7 +2971,8 @@ def sigma_clip_legacy(self, data, npt_rad=1024, npt_azim=512,
                                  dummy=dummy, delta_dummy=delta_dummy,
                                  correctSolidAngle=correctSolidAngle,
                                  polarization_factor=polarization_factor,
-                                 normalization_factor=normalization_factor,safe=safe)
+                                 normalization_factor=normalization_factor,
+                                 safe=safe)
         image = res2d.intensity
         if (method.impl_lower == "opencl"):
             if (method.algo_lower == "csr") and \
@@ -3086,8 +3087,9 @@ def sigma_clip_ng(self, data,
 
             ``|I - <I>| < thres * σ(I)``
 
-        This enforces a symmetric, bell-shaped distibution (i.e. gaussian-like) and is very good at extracting
-        background or amorphous isotropic scattering out of Bragg peaks.
+        This enforces a symmetric, bell-shaped distibution (i.e. gaussian-like)
+        and is very good at extracting background or amorphous isotropic scattering
+        out of Bragg peaks.
 
         :param data: input image as numpy array
         :param npt_rad: number of radial points

pyFAI/ext/splitBBoxCSC.pyx

@@ -37,7 +37,7 @@ Serial implementation based on a sparse CSC matrix multiplication
 
 __author__ = "Jérôme Kieffer"
 __contact__ = "[email protected]"
-__date__ = "08/09/2022"
+__date__ = "31/01/2023"
 __status__ = "stable"
 __license__ = "MIT"
 
@@ -184,7 +184,7 @@ class HistoBBox2d(CscIntegrator, SplitBBoxIntegrator):
         self.bin_centers1 = numpy.linspace(self.pos1_min + 0.5 * self.delta1,
                                            self.pos1_max - 0.5 * self.delta1,
                                            self.bins[1])
-        csc = self.calc_lut_2d().to_csr()
+        csc = sparse.csr_matrix(self.calc_lut_2d().to_csr()).tocsc()
         #Call the constructor of the parent class
         CscIntegrator.__init__(self, (csc.data, csc.indices, csc.indptr), self.size, numpy.prod(bins), empty or 0.0)
         self.lut_checksum = crc32(self.data)

pyFAI/ext/splitPixelFullCSC.pyx

@@ -35,7 +35,7 @@ Sparse matrix represented using the CompressedSparseColumn.
 
 __author__ = "Jérôme Kieffer"
 __contact__ = "[email protected]"
-__date__ = "09/09/2022"
+__date__ = "31/01/2023"
 __status__ = "stable"
 __license__ = "MIT"
 
@@ -169,7 +169,7 @@ class FullSplitCSC_2d(CscIntegrator, FullSplitIntegrator):
 
         csc = sparse.csr_matrix(self.calc_lut_2d().to_csr()).tocsc()
         #Call the constructor of the parent class
-        CscIntegrator.__init__(self, (csc.data, csc.indices, csc.indptr), self.pos.shape[0], self.bins, empty or 0.0)
+        CscIntegrator.__init__(self, (csc.data, csc.indices, csc.indptr), self.pos.shape[0], numpy.prod(bins), empty or 0.0)
 
         self.lut_checksum = crc32(self.data)
         self.lut_nbytes = sum([i.nbytes for i in self.lut])

pyFAI/gui/dialog/GeometryDialog.py

@@ -23,9 +23,9 @@
 #
 # ###########################################################################*/
 
-__authors__ = ["V. Valls"]
+__authors__ = ["V. Valls", "J. Kieffer"]
 __license__ = "MIT"
-__date__ = "03/02/2023"
+__date__ = "24/02/2023"
 
 from silx.gui import qt
 from ..model.GeometryModel import GeometryModel

pyFAI/gui/dialog/IntegrationMethodDialog.py

@@ -25,7 +25,7 @@
 
 __authors__ = ["V. Valls"]
 __license__ = "MIT"
-__date__ = "16/10/2020"
+__date__ = "31/01/2023"
 
 from silx.gui import qt
 from silx.gui import icons
@@ -46,6 +46,7 @@ class IntegrationMethodWidget(qt.QWidget):
         "histogram": "Histogram",
         "lut": "LUT",
         "csr": "CSR",
+        "csc": "CSC",
         "python": "Python",
         "cython": "Cython",
         "opencl": "OpenCL",
@@ -66,6 +67,7 @@ class IntegrationMethodWidget(qt.QWidget):
         "histogram": "Direct integration method with the lowest memory footprint but slower",
         "lut": "Sparse matrix based integration using a look-up table. Long initalization time and highest memory usage. Often slower than CSR",
         "csr": "Sparse matrix based integration using a a CSR (compressed sparse row) representation. Long initalization time and high memory usage, but the fastest for processing",
+        "csc": "Sparse matrix based integration using a a CSC (compressed sparse column) representation. Long initalization time and high memory usage. Single-threaded but faster processsing than histogram",
         "python": "Use a pure Python/numpy/scipy implementation. Slow but portable",
         "cython": "Use a Cython/C/C++ implementation. Fast and reliable default methods",
         "opencl": "Use an OpenCL implementation based on hardware accelerators. Fastest but hardware/driver dependant",

pyFAI/gui/tasks/IntegrationTask.py

@@ -1,7 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
 #
-# Copyright (C) 2016-2018 European Synchrotron Radiation Facility
+# Copyright (C) 2016-2023 European Synchrotron Radiation Facility
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -23,9 +23,9 @@
 #
 # ###########################################################################*/
 
-__authors__ = ["V. Valls"]
+__authors__ = ["V. Valls", "J. Kieffer"]
 __license__ = "MIT"
-__date__ = "05/05/2022"
+__date__ = "24/02/2023"
 
 import logging
 import numpy
@@ -40,6 +40,8 @@
 from pyFAI.azimuthalIntegrator import AzimuthalIntegrator
 from ..utils import unitutils
 from ..model.DataModel import DataModel
+# from ..model.GeometryModel import GeometryModel
+# from ..model.Fit2dGeometryModel import Fit2dGeometryModel
 from ..widgets.QuantityLabel import QuantityLabel
 from ..CalibrationContext import CalibrationContext
 from ... import units as core_units
@@ -56,6 +58,7 @@
 from pyFAI import method_registry
 from ..dialog import MessageBox
 from pyFAI.io import ponifile
+import pyFAI.geometry
 
 _logger = logging.getLogger(__name__)
 
@@ -100,13 +103,13 @@ def setValue(self, value):
 
 class IntegrationProcess(object):
 
-    def __init__(self, model):
-        self.__isValid = self._init(model)
+    def __init__(self, model, altGeometry=None):
+        self.__isValid = self._init(model, altGeometry)
         self.__resetZoomPolicy = None
         self.__method = None
         self.__errorMessage = None
 
-    def _init(self, model):
+    def _init(self, model, altGeometry=None):
         self.__isValid = True
         if model is None:
             return False
@@ -117,7 +120,10 @@ def _init(self, model):
         detector = model.experimentSettingsModel().detector()
         if detector is None:
             return
-        geometry = model.fittedGeometry()
+        if altGeometry:
+            geometry = altGeometry
+        else:
+            geometry = model.fittedGeometry()
         if not geometry.isValid():
             return False
         self.__nPointsAzimuthal = model.integrationSettingsModel().nPointsAzimuthal().value()
@@ -905,15 +911,15 @@ def _initGui(self):
 
         self.__integrationUpToDate = True
         self.__integrationResetZoomPolicy = None
-        method = method_registry.Method(666, "bbox", "csr", "cython", None)
+        method = method_registry.Method(666, "bbox", "histogram", "cython", None)
         self.__setMethod(method)
 
         positiveValidator = validators.IntegerAndEmptyValidator(self)
         positiveValidator.setBottom(1)
 
         self._radialPoints.setValidator(positiveValidator)
         self._azimuthalPoints.setValidator(positiveValidator)
-        self._radialUnit.setUnits(pyFAI.units.RADIAL_UNITS.values())
+        self._radialUnit.setUnits(core_units.RADIAL_UNITS.values())
         self.__polarizationModel = None
         self._polarizationFactorCheck.clicked[bool].connect(self.__polarizationFactorChecked)
         self.widgetShow.connect(self.__widgetShow)
@@ -985,7 +991,8 @@ def __widgetShow(self):
             self._integrateButton.executeCallable()
 
     def __integrate(self):
-        self.__integrationProcess = IntegrationProcess(self.model())
+        geometry = self._geometryTabs.geometryModel()
+        self.__integrationProcess = IntegrationProcess(self.model(), geometry)
         self.__integrationProcess.setMethod(self.__method)
 
         if self.__integrationResetZoomPolicy is not None:
@@ -1058,13 +1065,16 @@ def __fittedGeometryChanged(self):
         poniFile = self.model().experimentSettingsModel().poniFile()
         with poniFile.lockContext():
             poniFile.setSynchronized(False)
+        # Update displayed data:
+        self.__updateDisplayedGeometry()
 
     def __saveAsPoni(self):
         # FIXME test the validity of the geometry before opening the dialog
         dialog = createSaveDialog(self, "Save as PONI file", poni=True)
         # Disable the warning as the data is append to the file
         dialog.setOption(qt.QFileDialog.DontConfirmOverwrite, True)
-        poniFile = self.model().experimentSettingsModel().poniFile()
+        model = self.model()
+        poniFile = model.experimentSettingsModel().poniFile()
         previousPoniFile = poniFile.value()
         if previousPoniFile is not None:
             dialog.selectFile(previousPoniFile)
@@ -1080,21 +1090,19 @@ def __saveAsPoni(self):
         with poniFile.lockContext():
             poniFile.setValue(filename)
 
-        pyfaiGeometry = pyFAI.geometry.Geometry()
-
-        geometry = self.model().fittedGeometry()
-        pyfaiGeometry.dist = geometry.distance().value()
-        pyfaiGeometry.poni1 = geometry.poni1().value()
-        pyfaiGeometry.poni2 = geometry.poni2().value()
-        pyfaiGeometry.rot1 = geometry.rotation1().value()
-        pyfaiGeometry.rot2 = geometry.rotation2().value()
-        pyfaiGeometry.rot3 = geometry.rotation3().value()
-        pyfaiGeometry.wavelength = geometry.wavelength().value()
-
-        experimentSettingsModel = self.model().experimentSettingsModel()
+        geometry = self._geometryTabs.geometryModel()
+        experimentSettingsModel = model.experimentSettingsModel()
         detector = experimentSettingsModel.detector()
-        pyfaiGeometry.detector = detector
-
+        pyfaiGeometry = pyFAI.geometry.Geometry(
+            dist=geometry.distance().value(),
+            poni1=geometry.poni1().value(),
+            poni2=geometry.poni2().value(),
+            rot1=geometry.rotation1().value(),
+            rot2=geometry.rotation2().value(),
+            rot3=geometry.rotation3().value(),
+            wavelength=geometry.wavelength().value(),
+            detector=detector
+            )
         try:
             writer = ponifile.PoniFile(pyfaiGeometry)
             with open(filename, "wt") as fd:
@@ -1104,3 +1112,9 @@ def __saveAsPoni(self):
                 poniFile.setSynchronized(True)
         except Exception as e:
             MessageBox.exception(self, "Error while saving poni file", e, _logger)
+
+    def __updateDisplayedGeometry(self):
+        "Called after the fit"
+        experimentSettingsModel = self.model().experimentSettingsModel()
+        self._geometryTabs.setDetector(experimentSettingsModel.detector())
+        self._geometryTabs.setGeometryModel(self.model().fittedGeometry())