Merge pull request #2378 from EdgarGF93/sample_orientations_exif

Sample orientations exif

Author: kif

sandbox/test_grazingincidence.py

@@ -21,6 +21,17 @@
     data_file = UtilsTest.getimage("Y6.edf")
     data_2 = fabio.open(data_file).data
 
+    results = []
+    fig, axes = subplots(ncols=4, nrows=2)
+    for sample_orientation in range(1, 9):
+        res = fi_2.integrate2d_grazing_incidence(data=data_2, incident_angle=0.0, tilt_angle=0.0, sample_orientation=sample_orientation)
+        results.append(res)
+        plot2d(res, ax=axes.ravel()[sample_orientation-1])
+    plt.show()
+
+
+
+
     for fi, data in zip((fi_1, fi_2), (data_1, data_2)):
         res2d_1 = fi.integrate2d_grazing_incidence(data=data, incident_angle=0.0, tilt_angle=0.0, sample_orientation=1)
         res2d_2 = fi.integrate2d_grazing_incidence(data=data, incident_angle=0.2, tilt_angle=0.0, sample_orientation=1)

src/pyFAI/integrator/fiber.py

@@ -105,18 +105,39 @@ def __repr__(self, dist_unit="m", ang_unit="rad", wl_unit="m"):
         return f"{core_repr}\nIncident angle: {self.incident_angle:.2f}° Tilt angle {self.tilt_angle:.2f}° Sample orientation {self.sample_orientation}"
 
     @property
-    def incident_angle(self):
+    def incident_angle(self) -> float:
+        """Pitch angle: projection angle of the beam in the sample. Its rotation axis is the horizontal axis of the lab system.
+        """
         return self._cache_parameters.get('incident_angle', 0.0)
 
     @property
-    def tilt_angle(self):
+    def tilt_angle(self) -> float:
+        """Roll angle. Its rotation axis is the beam axis. Tilting of the horizon for grazing incidence in thin films.
+        """
         return self._cache_parameters.get('tilt_angle', 0.0)
 
     @property
-    def sample_orientation(self):
+    def sample_orientation(self) -> int:
+        """Orientation of the fiber axis according to EXIF orientation values
+
+        Sample orientations
+        1 - No changes are applied to the image
+        2 - Image is mirrored (flipped horizontally)
+        3 - Image is rotated 180 degrees
+        4 - Image is rotated 180 degrees and mirrored
+        5 - Image is mirrored and rotated 90 degrees counter clockwise
+        6 - Image is rotated 90 degrees counter clockwise
+        7 - Image is mirrored and rotated 90 degrees clockwise
+        8 - Image is rotated 90 degrees clockwise
+        """
         return self._cache_parameters.get('sample_orientation', 1)
 
     def reset_integrator(self, incident_angle, tilt_angle, sample_orientation):
+        """Reset the cache values for the gi/fiber parameters
+        :param incident_angle: tilting of the sample towards the beam (analog to rot2): in radians
+        :param tilt_angle: tilting of the sample orthogonal to the beam direction (analog to rot3): in radians
+        :param int sample_orientation: 1-8, orientation of the fiber axis according to EXIF orientation values (see def sample_orientation)
+        """
         reset = False
         if incident_angle != self.incident_angle:
             logger.info(f"Incident angle set to {incident_angle}. AzimuthalIntegrator will be reset.")
@@ -161,7 +182,7 @@ def integrate_fiber(self, data,
         :param bool vertical_integration: If True, integrates along unit_ip; if False, integrates along unit_oop
         :param incident_angle: tilting of the sample towards the beam (analog to rot2): in radians
         :param tilt_angle: tilting of the sample orthogonal to the beam direction (analog to rot3): in radians
-        :param int sample_orientation: 1-4, four different orientation of the fiber axis regarding the detector main axis, from 1 to 4 is +90º
+        :param int sample_orientation: 1-8, orientation of the fiber axis according to EXIF orientation values (see def sample_orientation)
         :param str filename: output filename in 2/3 column ascii format
         :param bool correctSolidAngle: correct for solid angle of each pixel if True
         :param ndarray mask: array (same size as image) with 1 for masked pixels, and 0 for valid pixels
@@ -299,7 +320,7 @@ def integrate2d_fiber(self, data,
         :param list oop_range: The lower and upper range of the out-of-plane unit. If not provided, range is simply (data.min(), data.max()). Values outside the range are ignored. Optional.
         :param incident_angle: tilting of the sample towards the beam (analog to rot2): in radians
         :param tilt_angle: tilting of the sample orthogonal to the beam direction (analog to rot3): in radians
-        :param int sample_orientation: 1-4, four different orientation of the fiber axis regarding the detector main axis, from 1 to 4 is +90º
+        :param int sample_orientation: 1-8, orientation of the fiber axis according to EXIF orientation values (see def sample_orientation)
         :param str filename: output filename in 2/3 column ascii format
         :param bool correctSolidAngle: correct for solid angle of each pixel if True
         :param ndarray mask: array (same size as image) with 1 for masked pixels, and 0 for valid pixels

src/pyFAI/test/test_fiber_integrator.py

@@ -488,107 +488,6 @@ def test_integrate1d_horizontal_deprecated_units(self):
         self.assertFalse(abs(res1d_ref.radial - res1d_deprecated.radial).max(), 0)
         self.assertFalse(abs(res1d_ref.intensity - res1d_deprecated.intensity).max(), 0)
 
-    def test_sample_orientation_equivalence(self):
-        incident_angle = 0.0
-        tilt_angle =0.0
-        npt_ip = 100
-        npt_oop = 100
-
-        threshold = 1.0
-
-        sample_orientation = 1
-        oop_range_1 = [-5,5]
-        ip_range_1 = [0,20]
-        res_so_1 = self.fi.integrate_grazing_incidence(data=self.data, npt_ip=npt_ip, npt_oop=npt_oop,
-                                                       ip_range=ip_range_1, oop_range=oop_range_1,
-                                                       incident_angle=incident_angle, tilt_angle=tilt_angle,
-                                                       sample_orientation=sample_orientation,
-                                                       vertical_integration=False,
-        )
-
-        sample_orientation = 2
-        ip_range_2 = [-5,5]
-        oop_range_2 = [0,20]
-        res_so_2 = self.fi.integrate_grazing_incidence(data=self.data, npt_ip=npt_ip, npt_oop=npt_oop,
-                                                       ip_range=ip_range_2, oop_range=oop_range_2,
-                                                       incident_angle=incident_angle, tilt_angle=tilt_angle,
-                                                       sample_orientation=sample_orientation,
-                                                       vertical_integration=True,
-        )
-
-        self.assertLess((abs(res_so_1.intensity) - abs(res_so_2.intensity)).max(), threshold)
-
-        sample_orientation = 3
-        oop_range_3 = [-5,5]
-        ip_range_3 = [-20,0]
-        res_so_3 = self.fi.integrate_grazing_incidence(data=self.data, npt_ip=npt_ip, npt_oop=npt_oop,
-                                                       ip_range=ip_range_3, oop_range=oop_range_3,
-                                                       incident_angle=incident_angle, tilt_angle=tilt_angle,
-                                                       sample_orientation=sample_orientation,
-                                                       vertical_integration=False,
-        )
-
-        self.assertLess((abs(res_so_3.intensity) - abs(res_so_2.intensity)).max(), threshold)
-
-        sample_orientation = 4
-        oop_range_4 = [-20,5]
-        ip_range_4 = [-5,5]
-        res_so_4 = self.fi.integrate_grazing_incidence(data=self.data, npt_ip=npt_ip, npt_oop=npt_oop,
-                                                       ip_range=ip_range_4, oop_range=oop_range_4,
-                                                       incident_angle=incident_angle, tilt_angle=tilt_angle,
-                                                       sample_orientation=sample_orientation,
-                                                       vertical_integration=True,
-        )
-
-        self.assertLess((abs(res_so_4.intensity) - abs(res_so_3.intensity)).max(), threshold)
-
-    def test_numexpr_equations(self):
-        incident_angle = 0.2
-        tilt_angle = -1.0
-        sample_orientation = 3
-
-        qhorz = get_unit_fiber(name="qxgi_nm^-1", incident_angle=incident_angle, tilt_angle=tilt_angle, sample_orientation=sample_orientation)
-        qvert = get_unit_fiber(name="qygi_nm^-1", incident_angle=incident_angle, tilt_angle=tilt_angle, sample_orientation=sample_orientation)
-        qbeam = get_unit_fiber(name="qzgi_nm^-1", incident_angle=incident_angle, tilt_angle=tilt_angle, sample_orientation=sample_orientation)
-        qip = get_unit_fiber(name="qip_nm^-1", incident_angle=incident_angle, tilt_angle=tilt_angle, sample_orientation=sample_orientation)
-        qoop = get_unit_fiber(name="qoop_nm^-1", incident_angle=incident_angle, tilt_angle=tilt_angle, sample_orientation=sample_orientation)
-
-        self.fi.reset()
-        arr_qhorz_fast = self.fi.array_from_unit(unit=qhorz)
-        arr_qvert_fast = self.fi.array_from_unit(unit=qvert)
-        arr_qbeam_fast = self.fi.array_from_unit(unit=qbeam)
-        arr_qip_fast = self.fi.array_from_unit(unit=qip)
-        arr_qoop_fast = self.fi.array_from_unit(unit=qoop)
-        res2d_fast = self.fi.integrate2d_grazing_incidence(data=self.data, unit_ip=qip, unit_oop=qoop)
-
-        qhorz.formula = None
-        qhorz.equation = qhorz._equation
-        qvert.formula = None
-        qvert.equation = qvert._equation
-        qbeam.formula = None
-        qbeam.equation = qbeam._equation
-        qip.formula = None
-        qip.equation = qip._equation
-        qoop.formula = None
-        qoop.equation = qoop._equation
-
-        self.fi.reset()
-        arr_qhorz_slow = self.fi.array_from_unit(unit=qhorz)
-        arr_qvert_slow = self.fi.array_from_unit(unit=qvert)
-        arr_qbeam_slow = self.fi.array_from_unit(unit=qbeam)
-        arr_qip_slow = self.fi.array_from_unit(unit=qip)
-        arr_qoop_slow = self.fi.array_from_unit(unit=qoop)
-        res2d_slow = self.fi.integrate2d_grazing_incidence(data=self.data, unit_ip=qip, unit_oop=qoop)
-
-        self.assertAlmostEqual((arr_qhorz_fast - arr_qhorz_slow).max(), 0.0)
-        self.assertAlmostEqual((arr_qvert_fast - arr_qvert_slow).max(), 0.0)
-        self.assertAlmostEqual((arr_qbeam_fast - arr_qbeam_slow).max(), 0.0)
-        self.assertAlmostEqual((arr_qip_fast - arr_qip_slow).max(), 0.0)
-        self.assertAlmostEqual((arr_qoop_fast - arr_qoop_slow).max(), 0.0)
-        self.assertAlmostEqual((res2d_fast.intensity - res2d_slow.intensity).max(), 0.0)
-        self.assertAlmostEqual((res2d_fast.radial - res2d_slow.radial).max(), 0.0)
-        self.assertAlmostEqual((res2d_fast.azimuthal - res2d_slow.azimuthal).max(), 0.0)
-
 def suite():
     testsuite = unittest.TestSuite()
     loader = unittest.defaultTestLoader.loadTestsFromTestCase