Merge pull request #2032 from kif/1957_pixel_corners

Register the number of pixel corners

doc/source/changelog.rst

@@ -1,12 +1,13 @@
 :Author: Jérôme Kieffer
-:Date: 10/01/2024
+:Date: 12/01/2024
 :Keywords: changelog
 
 Change-log of versions
 ======================
 
 2024.1 UNRELEASED
 -----------------
+- Expose the number of corners of a detector pixel
 - Support XRDML formt (compatibility with MAUD software)
 - Support pathlib for reading PONI files
 - Refactor `pyFAI-benchmark` tool (Thanks Edgar)

src/pyFAI/detectors/__init__.py

@@ -4,7 +4,7 @@
 #    Project: Azimuthal integration
 #             https://github.com/silx-kit/pyFAI
 #
-#    Copyright (C) 2014-2022 European Synchrotron Radiation Facility, Grenoble, France
+#    Copyright (C) 2014-2024 European Synchrotron Radiation Facility, Grenoble, France
 #
 #    Principal author:       Jérôme Kieffer ([email protected])
 #
@@ -34,7 +34,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "21/03/2022"
+__date__ = "12/01/2024"
 __status__ = "stable"
 
 

src/pyFAI/detectors/_adsc.py

@@ -4,7 +4,7 @@
 #    Project: Fast Azimuthal integration
 #             https://github.com/silx-kit/pyFAI
 #
-#    Copyright (C) 2017-2018 European Synchrotron Radiation Facility, Grenoble, France
+#    Copyright (C) 2017-2024 European Synchrotron Radiation Facility, Grenoble, France
 #
 #    Principal author:       Jérôme Kieffer ([email protected])
 #
@@ -37,7 +37,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "22/11/2023"
+__date__ = "12/01/2024"
 __status__ = "production"
 
 from ._common import Detector, Orientation

src/pyFAI/detectors/_common.py

@@ -34,7 +34,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "12/12/2023"
+__date__ = "12/01/2024"
 __status__ = "stable"
 
 import logging
@@ -100,14 +100,15 @@ class Detector(metaclass=DetectorMeta):
     Generic class representing a 2D detector
     """
     MANUFACTURER = None
-
+    CORNERS = 4
     force_pixel = False  # Used to specify pixel size should be defined by the class itself.
     aliases = []  # list of alternative names
     registry = {}  # list of  detectors ...
     uniform_pixel = True  # tells all pixels have the same size
     IS_FLAT = True  # this detector is flat
     IS_CONTIGUOUS = True  # No gaps: all pixels are adjacents, speeds-up calculation
-    API_VERSION = "1.0"
+    API_VERSION = "1.1"
+    # 1.1: support for CORNER attribute
 
     HAVE_TAPER = False
     """If true a spline file is mandatory to correct the geometry"""
@@ -756,6 +757,7 @@ def get_pixel_corners(self, correct_binning=False):
         if self._pixel_corners is None:
             with self._sem:
                 if self._pixel_corners is None:
+                    assert self.CORNERS == 4, "overwrite this method when hexagonal !"
                     # r1, r2 = self._calc_pixel_index_from_orientation(False)
                     # like numpy.ogrid
                     # d1 = expand2d(r1, self.shape[1] + 1, False)
@@ -790,6 +792,7 @@ def _rebin_pixel_corners(self):
             r1 = self._pixel_corners.shape[1] // self.shape[1]
             if r0 == 0 or r1 == 0:
                 raise RuntimeError("Cannot unbin an image ")
+            assert self.CORNERS==4, "not valid with hexagonal pixels"
             pixel_corners = numpy.zeros((self.shape[0], self.shape[1], 4, 3), dtype=numpy.float32)
             pixel_corners[:,:, 0,:] = self._pixel_corners[::r0,::r1, 0,:]
             pixel_corners[:,:, 1,:] = self._pixel_corners[r0 - 1::r0,::r1, 1,:]
@@ -815,7 +818,7 @@ def set_pixel_corners(self, ary):
             # Validation for the array
             assert ary.ndim == 4
             assert ary.shape[3] == 3  # 3 coordinates in Z Y X
-            assert ary.shape[2] >= 3  # at least 3 corners per pixel
+            assert ary.shape[2] == self.CORNERS  # at least 3 corners per pixel
 
             z = ary[..., 0]
             is_flat = (z.max() == z.min() == 0.0)
@@ -845,6 +848,7 @@ def save(self, filename):
             det_grp["API_VERSION"] = numpy.string_(self.API_VERSION)
             det_grp["IS_FLAT"] = self.IS_FLAT
             det_grp["IS_CONTIGUOUS"] = self.IS_CONTIGUOUS
+            det_grp["CORNERS"] = self.CORNERS
             if self.dummy is not None:
                 det_grp["dummy"] = self.dummy
             if self.delta_dummy is not None:
@@ -1208,6 +1212,7 @@ class NexusDetector(Detector):
         "aliases",
         "IS_FLAT",
         "IS_CONTIGUOUS",
+        "CORNERS"
         "force_pixel",
         "_filename",
         "uniform_pixel") + Detector._UNMUTABLE_ATTRS + Detector._MUTABLE_ATTRS
@@ -1239,6 +1244,11 @@ def load(self, filename):
                 raise RuntimeError("No detector definition in this file %s" % filename)
             name = posixpath.split(det_grp.name)[-1]
             self.aliases = [name.replace("_", " "), det_grp.name]
+            if "API_VERSION" in det_grp:
+                self.API_VERSION = det_grp["API_VERSION"][()].decode()
+                api = [int(i) for i in self.API_VERSION.split(".")]
+                if api>=[1,1] and "CORNERS" in det_grp:
+                    self.CORNERS = det_grp["CORNERS"][()]
             if "IS_FLAT" in det_grp:
                 self.IS_FLAT = det_grp["IS_FLAT"][()]
             if "IS_CONTIGUOUS" in det_grp:

src/pyFAI/detectors/_hexagonal.py

@@ -33,7 +33,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "21/11/2023"
+__date__ = "12/01/2024"
 __status__ = "production"
 
 
@@ -57,17 +57,18 @@ class HexDetector(Detector):
     uniform_pixel = False # ensures we use the array of position !
     IS_CONTIGUOUS = False
     IS_FLAT = True
+    CORNERS = 6
 
-    @staticmethod
-    def build_pixel_coordinates(shape, pitch=1):
+    @classmethod
+    def build_pixel_coordinates(cls, shape, pitch=1):
         """Build the 4D array with pixel coordinates for a detector composed of hexagonal-pixels
 
         :param shape: 2-tuple with size of the detector in number of pixels (y, x)
         :param pitch: the distance between two pixels
         :return: array with pixel coordinates
         """
         assert len(shape) == 2
-        ary = numpy.zeros(shape+(6, 3), dtype=numpy.float32)
+        ary = numpy.zeros(shape + (cls.CORNERS, 3), dtype=numpy.float32)
         sqrt3 = sqrt(3.0)
         h = 0.5*sqrt3
         r = numpy.linspace(0, 2, 7, endpoint=True)[:-1] - 0.5

src/pyFAI/io/ponifile.py

@@ -31,7 +31,7 @@
 __author__ = "Jérôme Kieffer"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "09/01/2024"
+__date__ = "15/01/2024"
 __docformat__ = 'restructuredtext'
 
 import collections
@@ -49,6 +49,7 @@
 
 
 class PoniFile(object):
+    API_VERSION = 2.1 # valid version are 1, 2, 2.1
 
     def __init__(self, data=None):
         self._detector = None
@@ -104,10 +105,24 @@ def read_from_dict(self, config):
         """Initialize this object using a dictionary.
 
         .. note:: The dictionary is versionned.
+        Version:
+        * 1: Historical version (i.e. unversioned)
+        * 2: store detector and detector_config instead of pixelsize1, pixelsize2 and splinefile
+        * 2.1: manage orientation of detector in detector_config
         """
-        version = int(config.get("poni_version", 1))
+        version = float(config.get("poni_version", 1))
         if "detector_config" in config:
-            version = max(version, 2)
+            if "orientation" in config["detector_config"]:
+                version = max(version, 2.1)
+            else:
+                version = max(version, 2)
+        if version >= 2 and "detector_config" not in config:
+            _logger.error("PoniFile claim to be version 2 but contains no `detector_config` !!!")
+
+        if version == 2.1 and "orientation" not in config.get("detector_config", {}):
+            _logger.error("PoniFile claim to be version 2.1 but contains no detector orientation !!!")
+        self.API_VERSION = version
+
         if version == 1:
             # Handle former version of PONI-file
             if "detector" in config:
@@ -134,7 +149,7 @@ def read_from_dict(self, config):
                 if config["splinefile"].lower() != "none":
                     self._detector.set_splineFile(config["splinefile"])
 
-        elif version == 2:
+        elif version in (2, 2.1):
                 detector_name = config["detector"]
                 detector_config = config["detector_config"]
                 self._detector = detectors.detector_factory(detector_name, detector_config)
@@ -195,26 +210,41 @@ def read_from_geometryModel(self, model: GeometryModel, detector=None):
 
     def write(self, fd):
         """Write this object to an open stream.
+
+        :param fd: file descriptor (opened file)
+        :return: nothing
         """
-        fd.write(("# Nota: C-Order, 1 refers to the Y axis,"
-                 " 2 to the X axis \n"))
-        fd.write("# Calibration done at %s\n" % time.ctime())
-        fd.write("poni_version: 2\n")
         detector = self.detector
-        fd.write("Detector: %s\n" % detector.__class__.__name__)
-        fd.write("Detector_config: %s\n" % json.dumps(detector.get_config()))
-
-        fd.write("Distance: %s\n" % self._dist)
-        fd.write("Poni1: %s\n" % self._poni1)
-        fd.write("Poni2: %s\n" % self._poni2)
-        fd.write("Rot1: %s\n" % self._rot1)
-        fd.write("Rot2: %s\n" % self._rot2)
-        fd.write("Rot3: %s\n" % self._rot3)
+        txt = ["# Nota: C-Order, 1 refers to the Y axis, 2 to the X axis",
+              f"# Calibration done at {time.ctime()}",
+              f"poni_version: {self.API_VERSION}",
+              f"Detector: {detector.__class__.__name__}"]
+        if self.API_VERSION == 1:
+            if not detector.force_pixel:
+                txt += [f"pixelsize1: {detector.pixel1}",
+                        f"pixelsize2: {detector.pixel2}"]
+            if detector.splineFile:
+                txt.append(f"splinefile: {detector.splineFile}")
+        elif self.API_VERSION >= 2:
+            detector_config = detector.get_config()
+            if self.API_VERSION == 2:
+                detector_config.pop("orientation")
+            txt.append(f"Detector_config: {json.dumps(detector_config)}")
+
+        txt += [f"Distance: {self._dist}",
+                f"Poni1: {self._poni1}",
+                f"Poni2: {self._poni2}",
+                f"Rot1: {self._rot1}",
+                f"Rot2: {self._rot2}",
+                f"Rot3: {self._rot3}"
+                ]
         if self._wavelength is not None:
-            fd.write("Wavelength: %s\n" % self._wavelength)
+            txt.append(f"Wavelength: {self._wavelength}")
+        txt.append("")
+        fd.write("\n".join(txt))
 
     def as_dict(self):
-        config = collections.OrderedDict([("poni_version", 2)])
+        config = collections.OrderedDict([("poni_version", self.API_VERSION)])
         config["detector"] = self.detector.__class__.__name__
         config["detector_config"] = self.detector.get_config()
         config["dist"] = self._dist

src/pyFAI/test/test_detector.py

@@ -33,7 +33,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT+"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "12/12/2023"
+__date__ = "12/01/2024"
 
 import os
 import shutil
@@ -210,12 +210,12 @@ def test_nexus_detector(self):
             if err2 > 1e-6:
                 logger.error("%s precision on pixel position 1 is better than 1µm, got %e", det_name, err2)
 
-            self.assertTrue(err1 < 1e-6, "%s precision on pixel position 1 is better than 1µm, got %e" % (det_name, err1))
-            self.assertTrue(err2 < 1e-6, "%s precision on pixel position 2 is better than 1µm, got %e" % (det_name, err2))
+            self.assertLess(err1, 1e-6, f"{det_name} precision on pixel position 1 is better than 1µm, got {err1:e}")
+            self.assertLess(err2, 1e-6, f"{det_name} precision on pixel position 2 is better than 1µm, got {err1:e}")
             if not det.IS_FLAT:
                 err = abs(r[2] - o[2]).max()
                 self.assertTrue(err < 1e-6, "%s precision on pixel position 3 is better than 1µm, got %e" % (det_name, err))
-
+            self.assertEqual(det.CORNERS, new_det.CORNERS, "Number of pixel corner is consistent")
         # check Pilatus with displacement maps
         # check spline
         # check SPD displacement
@@ -353,6 +353,8 @@ def test_displacements(self):
 
     def test_hexagonal_detector(self):
         pix = detector_factory("Pixirad1")
+        self.assertEqual(pix.CORNERS, 6, "detector has 6 corners")
+
         wl = 1e-10
         from ..calibrant import ALL_CALIBRANTS
         from ..azimuthalIntegrator import AzimuthalIntegrator