trxrdpy 3.3.0__tar.gz → 3.3.2__tar.gz

{trxrdpy-3.3.0 → trxrdpy-3.3.2}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: trxrdpy
-Version: 3.3.0
+Version: 3.3.2
 Summary: Python toolkit for time-resolved X-ray diffraction simulation and beamline-dependent analysis workflows.
 Author: Julio Guzman-Brambila
 License-Expression: CC-BY-4.0
 Project-URL: Homepage, https://github.com/julioguzmanb/XRDpy
 Project-URL: Repository, https://github.com/julioguzmanb/XRDpy
-Project-URL: Documentation, https://github.com/julioguzmanb/XRDpy
+Project-URL: Documentation, https://github.com/julioguzmanb/XRDpy/raw/main/docs/manual/XRDpy_manual.pdf
 Project-URL: DOI, https://doi.org/10.5281/zenodo.18634909
 Project-URL: Issues, https://github.com/julioguzmanb/XRDpy/issues
 Keywords: xrd,time-resolved xrd,pump-probe,x-ray diffraction,diffraction,materials science,simulation,beamline analysis,pyFAI
@@ -60,7 +60,7 @@ Source code: https://github.com/julioguzmanb/XRDpy
 
 ## Manual
 
-- **User manual PDF:** [`docs/manual/XRDpy_manual.pdf`](docs/manual/XRDpy_manual.pdf)
+- **User manual PDF:** [download the PDF](https://github.com/julioguzmanb/XRDpy/raw/main/docs/manual/XRDpy_manual.pdf)
 
 ---
 

{trxrdpy-3.3.0 → trxrdpy-3.3.2}/README.md

@@ -17,7 +17,7 @@ Source code: https://github.com/julioguzmanb/XRDpy
 
 ## Manual
 
-- **User manual PDF:** [`docs/manual/XRDpy_manual.pdf`](docs/manual/XRDpy_manual.pdf)
+- **User manual PDF:** [download the PDF](https://github.com/julioguzmanb/XRDpy/raw/main/docs/manual/XRDpy_manual.pdf)
 
 ---
 

{trxrdpy-3.3.0 → trxrdpy-3.3.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "trxrdpy"
-version = "3.3.0"
+version = "3.3.2"
 description = "Python toolkit for time-resolved X-ray diffraction simulation and beamline-dependent analysis workflows."
 readme = { file = "README.md", content-type = "text/markdown" }
 requires-python = ">=3.10"
@@ -69,7 +69,7 @@ trxrdpy-sim-gui = "trxrdpy.simulation.gui:main"
 [project.urls]
 Homepage = "https://github.com/julioguzmanb/XRDpy"
 Repository = "https://github.com/julioguzmanb/XRDpy"
-Documentation = "https://github.com/julioguzmanb/XRDpy"
+Documentation = "https://github.com/julioguzmanb/XRDpy/raw/main/docs/manual/XRDpy_manual.pdf"
 DOI = "https://doi.org/10.5281/zenodo.18634909"
 Issues = "https://github.com/julioguzmanb/XRDpy/issues"
 

{trxrdpy-3.3.0 → trxrdpy-3.3.2}/src/trxrdpy/analysis/calibration.py

@@ -509,7 +509,7 @@ def plot_detector_and_cake(
     npt_azim: int = 360,
     radial_range: Optional[Tuple[float, float]] = None,
     azimuthal_range: Tuple[float, float] = (-90.0, 90.0),
-    normalize: bool = True,
+    normalize: bool = False,
     q_norm_range: Tuple[float, float] = (2.65, 2.75),
     use_mask: bool = True,
     poni_path: Optional[Union[str, Path]] = None,
@@ -534,8 +534,9 @@ def plot_detector_and_cake(
     """Plot a bare calibration detector image beside its pyFAI 2D cake.
 
     The detector panel uses pixel coordinates. The cake panel uses q in Å⁻¹
-    and the package's display-coordinate azimuth convention. When
-    ``normalize`` is true, each azimuthal row is normalized independently over
+    and the package's display-coordinate azimuth convention. ``normalize`` is
+    false by default so the diagnostic cake matches pyFAI's raw display. When
+    true, each azimuthal row is normalized independently over
     ``q_norm_range``. ``use_mask`` controls whether the resolved EDF mask is
     passed to pyFAI. Detector x and y directions can be flipped independently.
 
@@ -550,7 +551,7 @@ def plot_detector_and_cake(
     azimuthal_range : tuple of float
         Package-coordinate azimuthal limits in degrees.
     normalize : bool
-        Normalize each cake row over ``q_norm_range``.
+        Normalize each cake row over ``q_norm_range`` when enabled.
     q_norm_range : tuple of float
         q interval used for row-wise normalization.
     use_mask : bool

{trxrdpy-3.3.0 → trxrdpy-3.3.2}/src/trxrdpy/analysis/common/azimint_utils.py

@@ -845,6 +845,10 @@ class AzimIntegrator:
                 part_intensity = np.asarray(result.intensity, dtype=float)
                 part_q = np.asarray(result.radial, dtype=float)
                 part_azimuth = np.asarray(result.azimuthal, dtype=float)
+                if hasattr(result, "count"):
+                    count = np.asarray(result.count, dtype=float)
+                    if count.shape == part_intensity.shape:
+                        part_intensity = np.where(count > 0.0, part_intensity, np.nan)
             else:
                 part_intensity = np.asarray(result[0], dtype=float)
                 part_q = np.asarray(result[1], dtype=float)

{trxrdpy-3.3.0 → trxrdpy-3.3.2}/src/trxrdpy/analysis/common/plot_utils.py

@@ -515,6 +515,13 @@ class DetectorCakePlotter:
         """Initialize the plotter with the shared analysis style."""
         self.style = style
 
+    @staticmethod
+    def _cmap_with_bad_color(cmap_name: str, bad_color: str = "#b3b3b3"):
+        """Return a colormap copy with masked values shown as detector-void gray."""
+        cmap = plt.get_cmap(str(cmap_name)).copy()
+        cmap.set_bad(bad_color)
+        return cmap
+
     @staticmethod
     def _display_options(
         data: np.ndarray,
@@ -630,7 +637,7 @@ class DetectorCakePlotter:
             detector_data,
             origin="lower",
             aspect="equal",
-            cmap=str(detector_cmap),
+            cmap=self._cmap_with_bad_color(str(detector_cmap)),
             **detector_options,
         )
         axes[0].set_title("Detector image", fontsize=self.style.title_fontsize)
@@ -642,12 +649,14 @@ class DetectorCakePlotter:
             axes[0].invert_yaxis()
         fig.colorbar(detector_artist, ax=axes[0], label="Intensity [a.u.]")
 
+        cake_bad_color = "#b3b3b3"
+        axes[1].set_facecolor(cake_bad_color)
         cake_artist = axes[1].pcolormesh(
             radial,
             angles,
             cake_data,
             shading="auto",
-            cmap=str(cake_cmap),
+            cmap=self._cmap_with_bad_color(str(cake_cmap), cake_bad_color),
             **cake_options,
         )
         axes[1].set_title("2D cake", fontsize=self.style.title_fontsize)

{trxrdpy-3.3.0 → trxrdpy-3.3.2}/src/trxrdpy/analysis/gui/main_window.py

@@ -1533,6 +1533,9 @@ class AnalysisMainWindow(QMainWindow):
             "calib_caked_ylim": self._line_state(calibration.get("caked_ylim", "")),
             "calib_caked_figure_title": self._line_state(calibration.get("caked_figure_title", "")),
             "calib_caked_save": self._check_state(calibration.get("caked_save", True)),
+            "calib_detector_cake_normalize": self._check_state(
+                calibration.get("detector_cake_normalize", False)
+            ),
             "calib_property_name": self._line_state(calibration.get("property_name", "pv_center")),
             "calib_property_only_success": self._check_state(calibration.get("property_only_success", True)),
             "calib_property_ylim": self._line_state(calibration.get("property_ylim", "")),

{trxrdpy-3.3.0 → trxrdpy-3.3.2}/src/trxrdpy/analysis/gui/tabs/calibration_tab.py

@@ -336,6 +336,10 @@ class CalibrationTab(QWidget):
         self.calib_detector_cake_use_mask.setChecked(True)
         cg.addWidget(self.calib_detector_cake_use_mask, 4, 0, 1, 2)
 
+        self.calib_detector_cake_normalize = QCheckBox("Normalize cake rows")
+        self.calib_detector_cake_normalize.setChecked(False)
+        cg.addWidget(self.calib_detector_cake_normalize, 4, 2, 1, 2)
+
         self.calib_detector_cake_invert_x = QCheckBox("Flip detector X axis")
         self.calib_detector_cake_invert_x.setChecked(False)
         cg.addWidget(self.calib_detector_cake_invert_x, 5, 0)
@@ -708,7 +712,7 @@ class CalibrationTab(QWidget):
                     name="azimuthal_range",
                     cast=float,
                 ),
-                normalize=self.calib_normalize.isChecked(),
+                normalize=self.calib_detector_cake_normalize.isChecked(),
                 q_norm_range=parse_tuple2(
                     self.calib_q_norm_range.text(),
                     name="q_norm_range",

{trxrdpy-3.3.0 → trxrdpy-3.3.2}/src/trxrdpy.egg-info/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: trxrdpy
-Version: 3.3.0
+Version: 3.3.2
 Summary: Python toolkit for time-resolved X-ray diffraction simulation and beamline-dependent analysis workflows.
 Author: Julio Guzman-Brambila
 License-Expression: CC-BY-4.0
 Project-URL: Homepage, https://github.com/julioguzmanb/XRDpy
 Project-URL: Repository, https://github.com/julioguzmanb/XRDpy
-Project-URL: Documentation, https://github.com/julioguzmanb/XRDpy
+Project-URL: Documentation, https://github.com/julioguzmanb/XRDpy/raw/main/docs/manual/XRDpy_manual.pdf
 Project-URL: DOI, https://doi.org/10.5281/zenodo.18634909
 Project-URL: Issues, https://github.com/julioguzmanb/XRDpy/issues
 Keywords: xrd,time-resolved xrd,pump-probe,x-ray diffraction,diffraction,materials science,simulation,beamline analysis,pyFAI
@@ -60,7 +60,7 @@ Source code: https://github.com/julioguzmanb/XRDpy
 
 ## Manual
 
-- **User manual PDF:** [`docs/manual/XRDpy_manual.pdf`](docs/manual/XRDpy_manual.pdf)
+- **User manual PDF:** [download the PDF](https://github.com/julioguzmanb/XRDpy/raw/main/docs/manual/XRDpy_manual.pdf)
 
 ---
 

{trxrdpy-3.3.0 → trxrdpy-3.3.2}/tests/test_calibration_2d_cake.py

@@ -23,6 +23,7 @@ class _FakeIntegrate2dResult:
         )
         self.radial = np.array([1.0, 2.0, 3.0])
         self.azimuthal = np.array([-75.0, -25.0])
+        self.count = np.ones_like(self.intensity)
 
 
 class _FakeAzimuthalIntegrator:
@@ -131,6 +132,41 @@ def test_integrate2d_accepts_no_mask_and_passes_none_to_pyfai():
     assert fake_ai.kwargs["mask"] is None
 
 
+def test_integrate2d_masks_pyfai_bins_without_contributing_pixels():
+    class CountAwareFakeAzimuthalIntegrator:
+        def integrate2d(self, image, **kwargs):
+            result = _FakeIntegrate2dResult()
+            result.intensity = np.array(
+                [
+                    [1.0, 999.0, 3.0],
+                    [4.0, 5.0, 6.0],
+                ],
+                dtype=float,
+            )
+            result.count = np.array(
+                [
+                    [1.0, 0.0, 1.0],
+                    [1.0, 1.0, 1.0],
+                ],
+                dtype=float,
+            )
+            return result
+
+    integrator = AzimIntegrator(npt=3, normalize=False, azim_offset_deg=-90.0)
+    integrator._ai = CountAwareFakeAzimuthalIntegrator()
+    integrator._mask = np.zeros((2, 2), dtype=np.uint8)
+
+    cake, _q, _azimuth = integrator.integrate2d(
+        np.ones((2, 2)),
+        npt_rad=3,
+        npt_azim=2,
+        azimuthal_range=(0.0, 90.0),
+    )
+
+    assert np.isnan(cake[0, 1])
+    np.testing.assert_allclose(cake[0, [0, 2]], [1.0, 3.0])
+
+
 def test_mask_file_is_converted_to_pyfai_boolean_mask(monkeypatch):
     class FakeFabioImage:
         data = np.array([[0, 2], [-1, 0]], dtype=np.int16)
@@ -285,6 +321,7 @@ def test_public_calibration_api_connects_context_data_to_plotter(monkeypatch, tm
     assert context.scan == 7
     assert context.kwargs["npt_rad"] == 5
     assert context.kwargs["npt_azim"] == 4
+    assert context.kwargs["normalize"] is False
     assert context.kwargs["use_mask"] is False
     assert plotter.args[0] is detector
     assert plotter.args[1] is cake